Clean_up_ECO_SBO.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "91c15cb6-8962-493a-9403-07c8e85dcf55",
   "metadata": {},
   "source": [
    "## Clean up model and add SBO and ECO Terms"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6504bb0c-9c4d-4938-95b1-405f8da30243",
   "metadata": {},
   "source": [
    "### Import and methods"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "b1c97788-97d2-430f-b5ad-a27cf384409f",
   "metadata": {},
   "outputs": [],
   "source": [
    "import cobra\n",
    "import pandas as pd\n",
    "import libsbml\n",
    "\n",
    "reader = libsbml.SBMLReader()\n",
    "writer = libsbml.SBMLWriter()\n",
    "\n",
    "model = cobra.io.read_sbml_model(\"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.xml\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "cd651385-fffa-43a6-bd65-07b7ff32faa6",
   "metadata": {},
   "outputs": [],
   "source": [
    "model.reactions.ATPM.annotation.update({\"sbo\": \"SBO:0000176\"})"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "78e28543-0843-44bd-9cb8-3033aceb7fed",
   "metadata": {},
   "source": [
    "### SBO Terms"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "583c508f-af1a-4db7-9818-abded4ee4cc9",
   "metadata": {},
   "source": [
    "#### Reactions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "416a9574-e8a8-4a90-8f1a-4056dbb45fbd",
   "metadata": {},
   "outputs": [],
   "source": [
    "for r in model.reactions:\n",
    "    if \"sbo\" not in r.annotation:\n",
    "        if r.id in model.exchanges or r.id.startswith(\"EX_\"):\n",
    "            r.annotation.update({\"sbo\": \"SBO:0000627\"})   # add exchange reactions\n",
    "        elif not r.reactants:\n",
    "            r.annotation.update({\"sbo\": \"SBO:0000632\"})   # add sink reactions\n",
    "        elif not r.products:\n",
    "            r.annotation.update({\"sbo\": \"SBO:0000628\"})   # add demand reactions\n",
    "        else:\n",
    "            bigg_ids = [m.id[:-2] for m in r.metabolites]\n",
    "            if len(bigg_ids) > len(set(bigg_ids)):\n",
    "                r.annotation.update({\"sbo\": \"SBO:0000185\"})   # add transport reactions\n",
    "            else:\n",
    "                r.annotation.update({\"sbo\": \"SBO:0000176\"})   # add metabolic reactions"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "50dc7a2b-658d-4b2d-942b-12644168494b",
   "metadata": {},
   "source": [
    "#### Metabolites"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "47219576-24fd-452c-89a8-96ac5c2ecc61",
   "metadata": {},
   "outputs": [],
   "source": [
    "for m in model.metabolites:\n",
    "    if \"sbo\" not in m.annotation:\n",
    "        m.annotation.update({\"sbo\": \"SBO:0000247\"})   # add metabolites"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4f5f54da-5df4-4592-8d40-2d90c1c42ff5",
   "metadata": {},
   "source": [
    "#### Genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "10c32c04-ce63-49e9-9134-be64ab8cf3ae",
   "metadata": {},
   "outputs": [],
   "source": [
    "for g in model.genes:\n",
    "    if \"sbo\" not in g.annotation:\n",
    "        g.annotation.update({\"sbo\": \"SBO:0000243\"})   # add genes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "86200f9a-ad54-4add-913a-15ef9825637c",
   "metadata": {},
   "outputs": [],
   "source": [
    "cobra.io.write_sbml_model(model, \"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.xml\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "eff69cef-8e2d-405c-a458-894bb89cb87e",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "=============================================================================================== test session starts ===============================================================================================\n",
      "platform linux -- Python 3.8.8, pytest-4.6.11, py-1.10.0, pluggy-0.13.1\n",
      "rootdir: /home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests\n",
      "plugins: anyio-3.3.0\n",
      "collected 145 items\n",
      "\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py ...FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.F.F......FF....FFFF.F.FF.FFF..                             [ 44%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py ......F........F.FFFFFF                                                                            [ 60%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py .F.....F.F                                                                                       [ 67%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py .ssssssssssssssssFFFFFFFFFF                                                                  [ 86%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_essentiality.py s                                                                                           [ 86%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_growth.py s                                                                                                 [ 87%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_matrix.py ....                                                                                              [ 90%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py FF                                                                                                  [ 91%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py FFFFFFFFsF.                                                                                          [ 99%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_thermodynamics.py .                                                                                         [100%]\n",
      "\n",
      "==================================================================================================== FAILURES =====================================================================================================\n",
      "______________________________________________________________________________ test_metabolite_annotation_overview[pubchem.compound] ______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 968 metabolites (100.00%) lack annotation for\n",
      "E     pubchem.compound:         10fthf_c, 12dag3p_BS_c, 12dgr120_c,\n",
      "E     12dgr120_p, 12dgr140_c, ...\n",
      "E   assert 968 == 0\n",
      "E    +  where 968 = len(['10fthf_c', '12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', ...])\n",
      "_______________________________________________________________________________ test_metabolite_annotation_overview[kegg.compound] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 359 metabolites (37.09%) lack annotation for\n",
      "E     kegg.compound:         12dag3p_BS_c, 12dgr120_c, 12dgr120_p,\n",
      "E     12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 359 == 0\n",
      "E    +  where 359 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "_______________________________________________________________________________ test_metabolite_annotation_overview[seed.compound] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 248 metabolites (25.62%) lack annotation for\n",
      "E     seed.compound:         12dag3p_BS_c, 12dgr120_c, 12dgr120_p,\n",
      "E     12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 248 == 0\n",
      "E    +  where 248 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "__________________________________________________________________________________ test_metabolite_annotation_overview[inchikey] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 295 metabolites (30.48%) lack annotation for inchikey:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 295 == 0\n",
      "E    +  where 295 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_overview[inchi] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 968 metabolites (100.00%) lack annotation for inchi:\n",
      "E     10fthf_c, 12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, ...\n",
      "E   assert 968 == 0\n",
      "E    +  where 968 = len(['10fthf_c', '12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', ...])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_overview[chebi] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 315 metabolites (32.54%) lack annotation for chebi:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 315 == 0\n",
      "E    +  where 315 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "____________________________________________________________________________________ test_metabolite_annotation_overview[hmdb] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 424 metabolites (43.80%) lack annotation for hmdb:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 424 == 0\n",
      "E    +  where 424 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "__________________________________________________________________________________ test_metabolite_annotation_overview[reactome] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 589 metabolites (60.85%) lack annotation for reactome:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 589 == 0\n",
      "E    +  where 589 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "_____________________________________________________________________________ test_metabolite_annotation_overview[metanetx.chemical] ______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 167 metabolites (17.25%) lack annotation for\n",
      "E     metanetx.chemical:         2mb_p_c, 2mba_c, 2mba_e, 2mpa_c, 2mpa_e,\n",
      "E     ...\n",
      "E   assert 167 == 0\n",
      "E    +  where 167 = len(['2mb_p_c', '2mba_c', '2mba_e', '2mpa_c', '2mpa_e', 'fe3pyovd_kt_e', ...])\n",
      "______________________________________________________________________________ test_metabolite_annotation_overview[bigg.metabolite] _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 147 metabolites (15.19%) lack annotation for\n",
      "E     bigg.metabolite:         aproa_c, id3acald_c, ind3ac_c, im4act_c,\n",
      "E     im4ac_c, ...\n",
      "E   assert 147 == 0\n",
      "E    +  where 147 = len(['aproa_c', 'id3acald_c', 'ind3ac_c', 'im4act_c', 'im4ac_c', 'imzacd_c', ...])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_overview[biocyc] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 301 metabolites (31.10%) lack annotation for biocyc:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 301 == 0\n",
      "E    +  where 301 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "_____________________________________________________________________________________ test_reaction_annotation_overview[rhea] _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 744 reactions (56.49%) lack annotation for rhea:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 744 == 0\n",
      "E    +  where 744 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_overview[kegg.reaction] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 843 reactions (64.01%) lack annotation for\n",
      "E     kegg.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR160tipp,\n",
      "E     12DGR161tipp, 12DGR180tipp, ...\n",
      "E   assert 843 == 0\n",
      "E    +  where 843 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_overview[seed.reaction] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 450 reactions (34.17%) lack annotation for\n",
      "E     seed.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR160tipp,\n",
      "E     12DGR161tipp, 12DGR180tipp, ...\n",
      "E   assert 450 == 0\n",
      "E    +  where 450 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "______________________________________________________________________________ test_reaction_annotation_overview[metanetx.reaction] _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 224 reactions (17.01%) lack annotation for\n",
      "E     metanetx.reaction:         13PPDH2, 2AACLPPEAT160, 2MBAt6, 2MPAt6,\n",
      "E     2OBUT_Et, ...\n",
      "E   assert 224 == 0\n",
      "E    +  where 224 = len(['13PPDH2', '2AACLPPEAT160', '2MBAt6', '2MPAt6', '2OBUT_Et', '4HBAt', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_overview[bigg.reaction] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 134 reactions (10.17%) lack annotation for\n",
      "E     bigg.reaction:         AGPATr_BS, ALATA_D, ALATA_D2, ALATA_L2,\n",
      "E     ALCD22_L, ...\n",
      "E   assert 134 == 0\n",
      "E    +  where 134 = len(['AGPATr_BS', 'ALATA_D', 'ALATA_D2', 'ALATA_L2', 'ALCD22_L', 'CYSK2_I', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_overview[reactome] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 1132 reactions (85.95%) lack annotation for reactome:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 1132 == 0\n",
      "E    +  where 1132 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_overview[ec-code] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 620 reactions (47.08%) lack annotation for ec-code:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 620 == 0\n",
      "E    +  where 620 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "____________________________________________________________________________________ test_reaction_annotation_overview[brenda] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 1317 reactions (100.00%) lack annotation for brenda:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 1317 == 0\n",
      "E    +  where 1317 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "____________________________________________________________________________________ test_reaction_annotation_overview[biocyc] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 730 reactions (55.43%) lack annotation for biocyc:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 730 == 0\n",
      "E    +  where 730 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_overview[refseq] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 10 genes (1.66%) lack annotation for refseq:\n",
      "E     spontaneous, WP_002838602_1, WP_012290557_1, FMG_RS06010, FMG_1297,\n",
      "E     ...\n",
      "E   assert 10 == 0\n",
      "E    +  where 10 = len(['spontaneous', 'WP_002838602_1', 'WP_012290557_1', 'FMG_RS06010', 'FMG_1297', 'FMG_0667', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_overview[uniprot] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 217 genes (36.11%) lack annotation for uniprot:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290371_1, ...\n",
      "E   assert 217 == 0\n",
      "E    +  where 217 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290371_1', 'spontaneous', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_overview[ecogene] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ecogene:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "________________________________________________________________________________ test_gene_product_annotation_overview[kegg.genes] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 10 genes (1.66%) lack annotation for kegg.genes:\n",
      "E     spontaneous, WP_002838602_1, WP_012290557_1, FMG_RS06010, FMG_1297,\n",
      "E     ...\n",
      "E   assert 10 == 0\n",
      "E    +  where 10 = len(['spontaneous', 'WP_002838602_1', 'WP_012290557_1', 'FMG_RS06010', 'FMG_1297', 'FMG_0667', ...])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_overview[ncbigi] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ncbigi:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_overview[ncbigene] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ncbigene:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_______________________________________________________________________________ test_gene_product_annotation_overview[ncbiprotein] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 217 genes (36.11%) lack annotation for ncbiprotein:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290371_1, ...\n",
      "E   assert 217 == 0\n",
      "E    +  where 217 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290371_1', 'spontaneous', ...])\n",
      "___________________________________________________________________________________ test_gene_product_annotation_overview[ccds] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ccds:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "___________________________________________________________________________________ test_gene_product_annotation_overview[hprd] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for hprd:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "___________________________________________________________________________________ test_gene_product_annotation_overview[asap] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for asap:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_____________________________________________________________________________ test_metabolite_annotation_wrong_ids[pubchem.compound] ______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:281: in test_metabolite_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no metabolite annotations for the pubchem.compound database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "_______________________________________________________________________________ test_metabolite_annotation_wrong_ids[seed.compound] _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:292: in test_metabolite_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 1 metabolite annotations (0.14%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the\n",
      "E     seed.compound         database: trdox_c\n",
      "E   assert 1 == 0\n",
      "E    +  where 1 = len(['trdox_c'])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_wrong_ids[inchi] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:281: in test_metabolite_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no metabolite annotations for the inchi database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "____________________________________________________________________________________ test_reaction_annotation_wrong_ids[rhea] _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 59 reaction annotations (4.48%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the rhea\n",
      "E     database: AEPabcpp, ARGabc, ASPabc, ASPabcpp, CA2abc, ...\n",
      "E   assert 59 == 0\n",
      "E    +  where 59 = len(['AEPabcpp', 'ARGabc', 'ASPabc', 'ASPabcpp', 'CA2abc', 'CA2abc1', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_wrong_ids[kegg.reaction] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 12 reaction annotations (0.91%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the\n",
      "E     kegg.reaction         database: AMALT1, AMALT2, AMALT3, HCO3E, LACZpp,\n",
      "E     ...\n",
      "E   assert 12 == 0\n",
      "E    +  where 12 = len(['AMALT1', 'AMALT2', 'AMALT3', 'HCO3E', 'LACZpp', 'MAL6PG', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_wrong_ids[ec-code] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 77 reaction annotations (5.85%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the ec-code\n",
      "E     database: 4ABUTD, 4HTHRS, AKGDH, AKGt2r, ALCD4, ...\n",
      "E   assert 77 == 0\n",
      "E    +  where 77 = len(['4ABUTD', '4HTHRS', 'AKGDH', 'AKGt2r', 'ALCD4', 'ALCD4y', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_wrong_ids[brenda] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:328: in test_reaction_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no reaction annotations for the brenda database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "___________________________________________________________________________________ test_reaction_annotation_wrong_ids[biocyc] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 5 reaction annotations (0.38%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the biocyc\n",
      "E     database: PHETYRr, TYRALAr, TYRGLUr, TYRTHRr, GLYTYRAP\n",
      "E   assert 5 == 0\n",
      "E    +  where 5 = len(['PHETYRr', 'TYRALAr', 'TYRGLUr', 'TYRTHRr', 'GLYTYRAP'])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_wrong_ids[refseq] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:386: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 591 gene annotations (98.34%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the refseq\n",
      "E     database: WP_012290939_1, WP_012290272_1, WP_002842355_1,\n",
      "E     WP_012291190_1, WP_012290992_1, ...\n",
      "E   assert 591 == 0\n",
      "E    +  where 591 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ecogene] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ecogene database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ncbigi] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ncbigi database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ncbigene] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ncbigene database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ccds] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ccds database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_wrong_ids[hprd] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the hprd database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_wrong_ids[asap] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the asap database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "____________________________________________________________________________________ test_gene_protein_reaction_rule_presence _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:206: in test_gene_protein_reaction_rule_presence\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: There are a total of 305 reactions (23.16%) without GPR:\n",
      "E     MDDCP2pp, GLYC3Ptex, FAO11, 2AGPE160tipp, 2AGPEAT180, ...\n",
      "E   assert 305 == 0\n",
      "E    +  where 305 = len(['MDDCP2pp', 'GLYC3Ptex', 'FAO11', '2AGPE160tipp', '2AGPEAT180', 'LCTSt3ipp', ...])\n",
      "______________________________________________________________________________________ test_transport_reaction_gpr_presence _______________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:499: in test_transport_reaction_gpr_presence\n",
      "    assert ann[\"metric\"] < 0.2, ann[\"message\"]\n",
      "E   AssertionError: There are a total of 106 transport reactions (31.27% of all\n",
      "E     transport reactions) without GPR:         2AGPE160tipp, ADEtex,\n",
      "E     DDCAt2pp, 2AGPE161tipp, 12DGR161tipp, ...\n",
      "E   assert 0.31268436578171094 < 0.2\n",
      "__________________________________________________________________________________________ test_find_unique_metabolites ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:555: in test_find_unique_metabolites\n",
      "    assert len(ann[\"data\"]) < len(model.metabolites), ann[\"message\"]\n",
      "E   AssertionError: Not counting the same entities in other compartments, there is a\n",
      "E     total of 968 (100.00%) unique metabolites in the model: dad_2_c,\n",
      "E     drib_c, dpcoa_e, 5mtr_c, gthrd_e, ...\n",
      "E   assert 968 < 968\n",
      "E    +  where 968 = len(['dad_2_c', 'drib_c', 'dpcoa_e', '5mtr_c', 'gthrd_e', 'glcn_c', ...])\n",
      "E    +  and   968 = len([<Metabolite 10fthf_c at 0x7ff064190820>, <Metabolite 12dag3p_BS_c at 0x7ff0641906a0>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff063cc1fa0>, <Metabolite tyrthr_c at 0x7ff063cc1fd0>, <Metabolite gly_tyr_c at 0x7ff063cc1f10>])\n",
      "E    +    where [<Metabolite 10fthf_c at 0x7ff064190820>, <Metabolite 12dag3p_BS_c at 0x7ff0641906a0>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff063cc1fa0>, <Metabolite tyrthr_c at 0x7ff063cc1fd0>, <Metabolite gly_tyr_c at 0x7ff063cc1f10>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff064169520>.metabolites\n",
      "_________________________________________________________________________________ test_find_duplicate_metabolites_in_compartments _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:584: in test_find_duplicate_metabolites_in_compartments\n",
      "    len(ann[\"data\"]), truncate(ann[\"data\"])))\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/utils.py:170: in truncate\n",
      "    return \", \".join(sequence)\n",
      "E   TypeError: sequence item 0: expected str instance, tuple found\n",
      "____________________________________________________________________________ test_find_reactions_with_partially_identical_annotations _____________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:624: in test_find_reactions_with_partially_identical_annotations\n",
      "    assert total == 0, ann[\"message\"]\n",
      "E   AssertionError: Based on annotations there are 137 different groups of overlapping\n",
      "E     annotation which corresponds to a total of 312 duplicated reactions in\n",
      "E     the model.\n",
      "E   assert 312 == 0\n",
      "__________________________________________________________________________________________ test_find_duplicate_reactions __________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:660: in test_find_duplicate_reactions\n",
      "    {}\"\"\".format(num, truncate(duplicates)))\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/utils.py:168: in truncate\n",
      "    return \", \".join(sequence[:LIST_SLICE] + [\"...\"])\n",
      "E   TypeError: sequence item 0: expected str instance, tuple found\n",
      "____________________________________________________________________________________ test_find_reactions_with_identical_genes _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:692: in test_find_reactions_with_identical_genes\n",
      "    assert num_dup == 0, ann[\"message\"]\n",
      "E   AssertionError: Based only on equal genes there are 154 different groups of\n",
      "E     identical reactions which corresponds to a total of 601\n",
      "E     duplicated reactions in the model.\n",
      "E   assert 601 == 0\n",
      "__________________________________________________________________________________________ test_find_medium_metabolites ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:713: in test_find_medium_metabolites\n",
      "    ann[\"metric\"] = len(ann[\"data\"]) / num_ex\n",
      "E   TypeError: unsupported operand type(s) for /: 'int' and 'list'\n",
      "________________________________________________________________________________________ test_biomass_consistency[Growth] _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py:121: in test_biomass_consistency\n",
      "    assert outcome, ann[\"message\"][reaction_id]\n",
      "E   AssertionError: The component molar mass of the biomass reaction Growth sums up to\n",
      "E     1.0300277967729958             which is outside of the 1e-03 margin\n",
      "E     from 1 mmol / g[CDW] / h.\n",
      "E   assert False\n",
      "________________________________________________________________________________________ test_fast_growth_default[Growth] _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py:370: in test_fast_growth_default\n",
      "    assert outcome, ann[\"message\"][reaction_id]\n",
      "E   AssertionError: Using the biomass reaction Growth and when the model is simulated on\n",
      "E     the provided default medium the growth rate is *lower* than that\n",
      "E     of the fastest bacteria. This is to be expected for             a\n",
      "E     majority of organisms.\n",
      "E   assert False\n",
      "________________________________________________________________________________ test_essential_precursors_not_in_biomass[Growth] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py:494: in test_essential_precursors_not_in_biomass\n",
      "    assert len(ann[\"data\"][reaction_id]) == 0, ann[\"message\"][reaction_id]\n",
      "E   AssertionError: Growth lacks a total of 1 essential metabolites         (1.72% of all\n",
      "E     biomass precursors). Specifically         these are: ['fmn_c'].\n",
      "E   assert 1 == 0\n",
      "E    +  where 1 = len(['fmn_c'])\n",
      "__________________________________________________________________________________________ test_reaction_charge_balance ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:158: in test_reaction_charge_balance\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 3 (0.26%) reactions are charge unbalanced with at\n",
      "E     least one of the metabolites not having a charge or the overall\n",
      "E     charge not equal to 0: BTS2, AGPATr_BS, G3POA_BS\n",
      "E   assert 3 == 0\n",
      "E    +  where 3 = len(['BTS2', 'AGPATr_BS', 'G3POA_BS'])\n",
      "___________________________________________________________________________________________ test_reaction_mass_balance ____________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:193: in test_reaction_mass_balance\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 2 (0.17%) reactions are mass unbalanced with at least\n",
      "E     one of the metabolites not having a formula or the overall mass not\n",
      "E     equal to 0: AGPATr_BS, G3POA_BS\n",
      "E   assert 2 == 0\n",
      "E    +  where 2 = len(['AGPATr_BS', 'G3POA_BS'])\n",
      "_____________________________________________________________________________________________ test_blocked_reactions ______________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:222: in test_blocked_reactions\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: There are 98 (7.44%) blocked reactions in         the model: EX_btn_e,\n",
      "E     EX_chol_e, EX_rmn_e, EX_spmd_e, EX_xyl__D_e, ...\n",
      "E   assert 98 == 0\n",
      "E    +  where 98 = len(['EX_btn_e', 'EX_chol_e', 'EX_rmn_e', 'EX_spmd_e', 'EX_xyl__D_e', 'ALDD22x', ...])\n",
      "__________________________________________________________________________________ test_find_stoichiometrically_balanced_cycles ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:246: in test_find_stoichiometrically_balanced_cycles\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: There are 111 (8.43%) reactions         which participate in SBC in\n",
      "E     the model: 13PPDH, 13PPDH2, 4ABUTD, ABUTD, ACCOAL, ...\n",
      "E   assert 111 == 0\n",
      "E    +  where 111 = len(['13PPDH', '13PPDH2', '4ABUTD', 'ABUTD', 'ACCOAL', 'ACKr', ...])\n",
      "________________________________________________________________________________________________ test_find_orphans ________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:271: in test_find_orphans\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 42 (4.34%) metabolites are not produced by any reaction\n",
      "E     of the model: cl_p, inost_c, aproa_c, id3acald_c, im4act_c, ...\n",
      "E   assert 42 == 0\n",
      "E    +  where 42 = len(['cl_p', 'inost_c', 'aproa_c', 'id3acald_c', 'im4act_c', 'imzacd_c', ...])\n",
      "_______________________________________________________________________________________________ test_find_deadends ________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:295: in test_find_deadends\n",
      "    assert ann[\"data\"] == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 45 (4.65%) metabolites are not consumed by any reaction\n",
      "E     of the model: 2ins_c, spmd_c, ind3ac_c, im4ac_c, imzac_c, ...\n",
      "E   assert ['2ins_c', 'spmd_c', 'ind3ac_c', 'im4ac_c', 'imzac_c', '4aabutn_c', ...] == 0\n",
      "_____________________________________________________________________________________________ test_find_disconnected ______________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:319: in test_find_disconnected\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 5 (0.52%) metabolites are not associated with any\n",
      "E     reaction of the model: 3php_c, pa160140_c, pa160180_c, pa160205n3_c,\n",
      "E     pa160226n3_c\n",
      "E   assert 5 == 0\n",
      "E    +  where 5 = len(['3php_c', 'pa160140_c', 'pa160180_c', 'pa160205n3_c', 'pa160226n3_c'])\n",
      "_______________________________________________________________________________ test_find_metabolites_not_produced_with_open_bounds _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:349: in test_find_metabolites_not_produced_with_open_bounds\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 250 (25.83%) metabolites cannot be produced in complete\n",
      "E     medium: 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr161_c,\n",
      "E     ...\n",
      "E   assert 250 == 0\n",
      "E    +  where 250 = len(['12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr161_c', '12dgr161_p', ...])\n",
      "_______________________________________________________________________________ test_find_metabolites_not_consumed_with_open_bounds _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:379: in test_find_metabolites_not_consumed_with_open_bounds\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 255 (26.34%) metabolites cannot be consumed in complete\n",
      "E     medium: 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr161_c,\n",
      "E     ...\n",
      "E   assert 255 == 0\n",
      "E    +  where 255 = len(['12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr161_c', '12dgr161_p', ...])\n",
      "______________________________________________________________________________ test_find_reactions_unbounded_flux_default_condition _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:413: in test_find_reactions_unbounded_flux_default_condition\n",
      "    assert ann[\"metric\"] <= 0.1, ann[\"message\"]\n",
      "E   AssertionError:  A fraction of 22.32% of the non-blocked reactions (in total 98\n",
      "E     reactions) can carry unbounded flux in the default model\n",
      "E     condition. Unbounded reactions may be involved in\n",
      "E     thermodynamically infeasible cycles: 13PPDH, 13PPDH2, 4ABUTD, ABUTD,\n",
      "E     ACCOAL, ...\n",
      "E   assert 0.22323462414578588 <= 0.1\n",
      "_________________________________________________________________________________________________ test_sbml_level _________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py:39: in test_sbml_level\n",
      "    sbml_version[0], sbml_version[1])\n",
      "E   TypeError: 'NoneType' object is not subscriptable\n",
      "________________________________________________________________________________________________ test_fbc_presence ________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py:66: in test_fbc_presence\n",
      "    fbc_present = sbml_version[2] is not None\n",
      "E   TypeError: 'NoneType' object is not subscriptable\n",
      "__________________________________________________________________________________________ test_metabolite_sbo_presence ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:58: in test_metabolite_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.metabolites), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 metabolites (0.00%) lack annotation with any type\n",
      "E     of SBO term:\n",
      "E   assert 0 == 968\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   968 = len([<Metabolite 10fthf_c at 0x7ff064190820>, <Metabolite 12dag3p_BS_c at 0x7ff0641906a0>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff063cc1fa0>, <Metabolite tyrthr_c at 0x7ff063cc1fd0>, <Metabolite gly_tyr_c at 0x7ff063cc1f10>])\n",
      "E    +    where [<Metabolite 10fthf_c at 0x7ff064190820>, <Metabolite 12dag3p_BS_c at 0x7ff0641906a0>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff063cc1fa0>, <Metabolite tyrthr_c at 0x7ff063cc1fd0>, <Metabolite gly_tyr_c at 0x7ff063cc1f10>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff064169520>.metabolites\n",
      "___________________________________________________________________________________________ test_reaction_sbo_presence ____________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:88: in test_reaction_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.reactions), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 reactions (0.00%) lack annotation with any type\n",
      "E     of SBO term:\n",
      "E   assert 0 == 1317\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   1317 = len([<Reaction 12DGR120tipp at 0x7ff063c92a60>, <Reaction 12DGR140tipp at 0x7ff063ba0ca0>, <Reaction 12DGR160tipp at 0x7ff...ff062fdef10>, <Reaction KAS8 at 0x7ff062fded30>, <Reaction NNDPR at 0x7ff062fdefd0>, <Reaction PPND at 0x7ff062f7af40>])\n",
      "E    +    where [<Reaction 12DGR120tipp at 0x7ff063c92a60>, <Reaction 12DGR140tipp at 0x7ff063ba0ca0>, <Reaction 12DGR160tipp at 0x7ff...ff062fdef10>, <Reaction KAS8 at 0x7ff062fded30>, <Reaction NNDPR at 0x7ff062fdefd0>, <Reaction PPND at 0x7ff062f7af40>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff064169520>.reactions\n",
      "_____________________________________________________________________________________________ test_gene_sbo_presence ______________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:117: in test_gene_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.genes), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 genes (0.00%) lack annotation with any type of\n",
      "E     SBO term:\n",
      "E   assert 0 == 601\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   601 = len([<Gene WP_012290939_1 at 0x7ff063c929a0>, <Gene WP_012290272_1 at 0x7ff063c92a00>, <Gene WP_002842355_1 at 0x7ff063c92...7ff063ba01c0>, <Gene FMG_0827 at 0x7ff063ba0b80>, <Gene FMG_1032 at 0x7ff063ba0b50>, <Gene FMG_0500 at 0x7ff063ba0c70>])\n",
      "E    +    where [<Gene WP_012290939_1 at 0x7ff063c929a0>, <Gene WP_012290272_1 at 0x7ff063c92a00>, <Gene WP_002842355_1 at 0x7ff063c92...7ff063ba01c0>, <Gene FMG_0827 at 0x7ff063ba0b80>, <Gene FMG_1032 at 0x7ff063ba0b50>, <Gene FMG_0500 at 0x7ff063ba0c70>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff064169520>.genes\n",
      "__________________________________________________________________________________ test_metabolic_reaction_specific_sbo_presence __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:150: in test_metabolic_reaction_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(pure), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 metabolic reactions (0.00% of all purely\n",
      "E     metabolic reactions) lack annotation with the SBO term\n",
      "E     \"SBO:0000176\" for 'biochemical reaction':\n",
      "E   assert 0 == 818\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   818 = len({<Reaction DCMPDA at 0x7ff0638f0070>, <Reaction 2AGPEAT180 at 0x7ff063b50130>, <Reaction NAMNPP at 0x7ff063038160>, <Reaction G1PP at 0x7ff06381fd30>, <Reaction ACKr at 0x7ff063b50220>, <Reaction DAGK140 at 0x7ff063958220>, ...})\n",
      "__________________________________________________________________________________ test_transport_reaction_specific_sbo_presence __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:188: in test_transport_reaction_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(transports), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 metabolic reactions (0.00% of all transport\n",
      "E     reactions) lack annotation with one of the SBO terms: ['SBO:0000185',\n",
      "E     'SBO:0000588', 'SBO:0000587', 'SBO:0000655', 'SBO:0000654',\n",
      "E     'SBO:0000660', 'SBO:0000659', 'SBO:0000657', 'SBO:0000658'] for\n",
      "E     'biochemical reaction':\n",
      "E   assert 0 == 339\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   339 = len({<Reaction PTRCORNt7 at 0x7ff063328040>, <Reaction 2AGPE160tipp at 0x7ff063b500a0>, <Reaction ADEtex at 0x7ff063b50640>, <Reaction BTNt at 0x7ff0639e8790>, <Reaction ASPabcpp at 0x7ff0639e8850>, <Reaction PTRCabc at 0x7ff063328910>, ...})\n",
      "______________________________________________________________________________________ test_metabolite_specific_sbo_presence ______________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:218: in test_metabolite_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.metabolites), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 transport reactions (0.00% of all metabolites)\n",
      "E     lack annotation with the SBO term \"SBO:0000247\" for\n",
      "E     'simple chemical':\n",
      "E   assert 0 == 968\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   968 = len([<Metabolite 10fthf_c at 0x7ff064190820>, <Metabolite 12dag3p_BS_c at 0x7ff0641906a0>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff063cc1fa0>, <Metabolite tyrthr_c at 0x7ff063cc1fd0>, <Metabolite gly_tyr_c at 0x7ff063cc1f10>])\n",
      "E    +    where [<Metabolite 10fthf_c at 0x7ff064190820>, <Metabolite 12dag3p_BS_c at 0x7ff0641906a0>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff063cc1fa0>, <Metabolite tyrthr_c at 0x7ff063cc1fd0>, <Metabolite gly_tyr_c at 0x7ff063cc1f10>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff064169520>.metabolites\n",
      "_________________________________________________________________________________________ test_gene_specific_sbo_presence _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:248: in test_gene_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.genes), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 genes (0.00% of all genes) lack             annotation\n",
      "E     with the SBO term \"SBO:0000243\" for             'gene':\n",
      "E   assert 0 == 601\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   601 = len([<Gene WP_012290939_1 at 0x7ff063c929a0>, <Gene WP_012290272_1 at 0x7ff063c92a00>, <Gene WP_002842355_1 at 0x7ff063c92...7ff063ba01c0>, <Gene FMG_0827 at 0x7ff063ba0b80>, <Gene FMG_1032 at 0x7ff063ba0b50>, <Gene FMG_0500 at 0x7ff063ba0c70>])\n",
      "E    +    where [<Gene WP_012290939_1 at 0x7ff063c929a0>, <Gene WP_012290272_1 at 0x7ff063c92a00>, <Gene WP_002842355_1 at 0x7ff063c92...7ff063ba01c0>, <Gene FMG_0827 at 0x7ff063ba0b80>, <Gene FMG_1032 at 0x7ff063ba0b50>, <Gene FMG_0500 at 0x7ff063ba0c70>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff064169520>.genes\n",
      "_______________________________________________________________________________________ test_exchange_specific_sbo_presence _______________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:290: in test_exchange_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(exchanges), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 exchange reactions (0.00% of all exchange\n",
      "E     reactions) lack annotation with the SBO term \"SBO:0000627\" for\n",
      "E     'exchange reaction':\n",
      "E   assert 0 == 157\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   157 = len([<Reaction EX_14glucan_e at 0x7ff063175310>, <Reaction EX_15dap_e at 0x7ff0631acbe0>, <Reaction EX_26dap__M_e at 0x7ff...Reaction EX_atp_e at 0x7ff063001d90>, <Reaction EX_pan4p_e at 0x7ff063001f40>, <Reaction EX_dpcoa_e at 0x7ff063001eb0>])\n",
      "_________________________________________________________________________________________ test_sink_specific_sbo_presence _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:376: in test_sink_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(sinks), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 genes (0.00% of all sink reactions) lack\n",
      "E     annotation with the SBO term \"SBO:0000632\" for         'sink\n",
      "E     reaction':\n",
      "E   assert 0 == 2\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   2 = len([<Reaction sink_lipopb_c at 0x7ff0631db9a0>, <Reaction sink_mobd_c at 0x7ff063175580>])\n",
      "================================================================================================ warnings summary =================================================================================================\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/support/thermodynamics.py:23\n",
      "  /home/salatan/anaconda3/lib/python3.8/site-packages/memote/support/thermodynamics.py:23: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working\n",
      "    from collections import Iterable, defaultdict\n",
      "\n",
      "-- Docs: https://docs.pytest.org/en/latest/warnings.html\n",
      "========================================================================== 77 failed, 49 passed, 19 skipped, 1 warnings in 23.33 seconds ==========================================================================\n"
     ]
    }
   ],
   "source": [
    "import memote\n",
    "# Make memote report\n",
    "result = memote.test_model(model, results=True)  #, skip=[\"test_find_metabolites_not_produced_with_open_bounds\"])\n",
    "report = memote.snapshot_report(result[1], config=None, html=True)\n",
    "with open(\"2.2/memote-reports/report.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.html\", \"w\") as handle:\n",
    "    handle.write(report)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f81214d3-a59d-45f5-8b88-35a1931d0ff6",
   "metadata": {},
   "source": [
    "### ECO-Terms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "367708f7-3e62-4ede-89c9-833a6f5d2aa5",
   "metadata": {},
   "outputs": [],
   "source": [
    "def add_eco_annotation(model, lnk, s_id, element):  \n",
    "    c = libsbml.CVTerm()\n",
    "    c.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER)\n",
    "    c.setBiologicalQualifierType(libsbml.BQB_IS_DESCRIBED_BY)\n",
    "    c.addResource(lnk)\n",
    "\n",
    "    if element == \"species\":\n",
    "        list_cv = [model.getSpecies(s_id).getCVTerm(i) for i in range(model.getSpecies(s_id).getNumCVTerms())]\n",
    "        if not c in list_cv:     # eliminate duplicates\n",
    "            model.getSpecies(s_id).addCVTerm(c)\n",
    "            \n",
    "    elif element == \"reaction\":\n",
    "        list_cv = [model.getReaction(s_id).getCVTerm(i) for i in range(model.getReaction(s_id).getNumCVTerms())]\n",
    "        if not c in list_cv:\n",
    "            model.getReaction(s_id).addCVTerm(c)\n",
    "            \n",
    "    elif element == \"gene\":\n",
    "        list_cv = [model.getPlugin(\"fbc\").getGeneProduct(s_id).getCVTerm(i) for i in range(model.getPlugin(\"fbc\").getGeneProduct(s_id).getNumCVTerms())]\n",
    "        if not c in list_cv:\n",
    "            model.getPlugin(\"fbc\").getGeneProduct(s_id).addCVTerm(c)\n",
    "    \n",
    "    return model"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "304f94c7-56ea-4400-9a87-a194d8429b26",
   "metadata": {},
   "outputs": [],
   "source": [
    "doc = reader.readSBML(\"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.xml\")\n",
    "model = doc.getModel()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "598e72e4-7e69-4a12-9356-86a43444ddec",
   "metadata": {
    "tags": []
   },
   "outputs": [],
   "source": [
    "manually_curated = pd.read_csv(\"2.2/tables/manually_curated_all.tsv\", sep=\"\\t\",header=None)\n",
    "manually_curated = list(manually_curated[0])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "bcdfba11-1a0d-4f7a-9370-87deacb57b43",
   "metadata": {},
   "outputs": [],
   "source": [
    "blast_evidence = [\"THRD_L_1\",\"BZDIOLDH\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "8eb649ae-99d9-4f19-8a5c-71f8b6b456dd",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1166\n"
     ]
    }
   ],
   "source": [
    "model_draft = cobra.io.read_sbml_model(\"2.2/finegoldia_magna_ATCC_29328_2.2.xml\")\n",
    "print(len(model_draft.reactions))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "0d34ee97-d6e6-4f6a-9d83-bf3ad5deab7a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "['NNDPR', 'DAPDC', 'KAS13', 'KARA2', 'DHAD2', 'KAS8', 'KAS7', 'ASPO2', 'ACHBS', 'BZ12DOX', 'PPND']\n"
     ]
    }
   ],
   "source": [
    "model_bgf = cobra.io.read_sbml_model(\"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.xml\")\n",
    "model_gf = cobra.io.read_sbml_model(\"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.xml\")\n",
    "\n",
    "reac_ids_bgf = [r.id for r in model_bgf.reactions]\n",
    "reac_ids_gf = [r.id for r in model_gf.reactions]\n",
    "added_automated_gf = list(set(reac_ids_gf) - set(reac_ids_bgf))\n",
    "print(added_automated_gf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "7f29210a-cdfb-4741-8902-32cf922c1e89",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "100%|██████████| 968/968 [00:00<00:00, 17702.42it/s]\n",
      "100%|██████████| 1317/1317 [00:00<00:00, 13802.40it/s]\n",
      "100%|██████████| 601/601 [00:00<00:00, 14282.59it/s]\n"
     ]
    }
   ],
   "source": [
    "from tqdm import tqdm\n",
    "for i in tqdm(range(model.getNumSpecies())):\n",
    "    s_id = model.getSpecies(i).getId()\n",
    "    if s_id in manually_curated:\n",
    "        lnk = \"https://identifiers.org/ECO:0007759\"\n",
    "    elif s_id in blast_evidence:\n",
    "        lnk = \"https://identifiers.org/ECO:0000031\"\n",
    "    elif s_id in model_draft.metabolites:\n",
    "        lnk = \"https://identifiers.org/ECO:0007482\" # biological system reconstruction evidence based on homology evidence used in automatic assertion\n",
    "    elif s_id in added_automated_gf:\n",
    "        lnk = \"https://identifiers.org/ECO:0000363\" # computational inference used in automatic assertion\n",
    "    else:\n",
    "        lnk = \"https://identifiers.org/ECO:0007636\"\n",
    "    model = add_eco_annotation(model, lnk, s_id, \"species\")\n",
    "    \n",
    "for i in tqdm(range(model.getNumReactions())):\n",
    "    s_id = model.getReaction(i).getId()\n",
    "    if s_id in manually_curated:\n",
    "        lnk = \"https://identifiers.org/ECO:0007759\"\n",
    "    elif s_id in blast_evidence:\n",
    "        lnk = \"https://identifiers.org/ECO:0000031\"\n",
    "    elif s_id in model_draft.reactions:\n",
    "        lnk = \"https://identifiers.org/ECO:0007482\"\n",
    "    elif s_id in added_automated_gf:\n",
    "        lnk = \"https://identifiers.org/ECO:0000363\"\n",
    "    else:\n",
    "        lnk = \"https://identifiers.org/ECO:0007636\"\n",
    "    model = add_eco_annotation(model, lnk, s_id, \"reaction\")\n",
    "        \n",
    "for i in tqdm(range(model.getPlugin(\"fbc\").getNumGeneProducts())):\n",
    "    s_id = model.getPlugin(\"fbc\").getGeneProduct(i).getId()\n",
    "    if s_id in manually_curated:\n",
    "        lnk = \"https://identifiers.org/ECO:0007759\"\n",
    "    elif s_id in blast_evidence:\n",
    "        lnk = \"https://identifiers.org/ECO:0000031\"\n",
    "    elif s_id in model_draft.genes:\n",
    "        lnk = \"https://identifiers.org/ECO:0007482\"\n",
    "    elif s_id in added_automated_gf:\n",
    "        lnk = \"https://identifiers.org/ECO:0000363\"\n",
    "    else:\n",
    "        lnk = \"https://identifiers.org/ECO:0007636\"\n",
    "    model = add_eco_annotation(model, lnk, s_id, \"gene\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "28ee0c9a-df9b-4956-bc1d-eb8fe9334347",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# Saving new model\n",
    "doc.setModel(model)\n",
    "writer.writeSBML(doc, \"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.xml\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "ac36303d-ce1b-4119-a3ae-062655bd1558",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "=============================================================================================== test session starts ===============================================================================================\n",
      "platform linux -- Python 3.8.8, pytest-4.6.11, py-1.10.0, pluggy-0.13.1\n",
      "rootdir: /home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests\n",
      "plugins: anyio-3.3.0\n",
      "collected 145 items\n",
      "\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py ...FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF.F.F......FF....FFFF.F.FF.FFF..                             [ 44%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py ......F........F.FFFFFF                                                                            [ 60%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py .F.....F.F                                                                                       [ 67%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py .ssssssssssssssssFFFFFFFFFF                                                                  [ 86%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_essentiality.py s                                                                                           [ 86%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_growth.py s                                                                                                 [ 87%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_matrix.py ....                                                                                              [ 90%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py FF                                                                                                  [ 91%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py FFFFFFFFsF.                                                                                          [ 99%]\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_thermodynamics.py .                                                                                         [100%]\n",
      "\n",
      "==================================================================================================== FAILURES =====================================================================================================\n",
      "______________________________________________________________________________ test_metabolite_annotation_overview[pubchem.compound] ______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 968 metabolites (100.00%) lack annotation for\n",
      "E     pubchem.compound:         10fthf_c, 12dag3p_BS_c, 12dgr120_c,\n",
      "E     12dgr120_p, 12dgr140_c, ...\n",
      "E   assert 968 == 0\n",
      "E    +  where 968 = len(['10fthf_c', '12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', ...])\n",
      "_______________________________________________________________________________ test_metabolite_annotation_overview[kegg.compound] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 359 metabolites (37.09%) lack annotation for\n",
      "E     kegg.compound:         12dag3p_BS_c, 12dgr120_c, 12dgr120_p,\n",
      "E     12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 359 == 0\n",
      "E    +  where 359 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "_______________________________________________________________________________ test_metabolite_annotation_overview[seed.compound] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 248 metabolites (25.62%) lack annotation for\n",
      "E     seed.compound:         12dag3p_BS_c, 12dgr120_c, 12dgr120_p,\n",
      "E     12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 248 == 0\n",
      "E    +  where 248 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "__________________________________________________________________________________ test_metabolite_annotation_overview[inchikey] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 295 metabolites (30.48%) lack annotation for inchikey:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 295 == 0\n",
      "E    +  where 295 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_overview[inchi] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 968 metabolites (100.00%) lack annotation for inchi:\n",
      "E     10fthf_c, 12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, ...\n",
      "E   assert 968 == 0\n",
      "E    +  where 968 = len(['10fthf_c', '12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', ...])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_overview[chebi] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 315 metabolites (32.54%) lack annotation for chebi:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 315 == 0\n",
      "E    +  where 315 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "____________________________________________________________________________________ test_metabolite_annotation_overview[hmdb] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 424 metabolites (43.80%) lack annotation for hmdb:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 424 == 0\n",
      "E    +  where 424 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "__________________________________________________________________________________ test_metabolite_annotation_overview[reactome] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 589 metabolites (60.85%) lack annotation for reactome:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 589 == 0\n",
      "E    +  where 589 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "_____________________________________________________________________________ test_metabolite_annotation_overview[metanetx.chemical] ______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 167 metabolites (17.25%) lack annotation for\n",
      "E     metanetx.chemical:         2mb_p_c, 2mba_c, 2mba_e, 2mpa_c, 2mpa_e,\n",
      "E     ...\n",
      "E   assert 167 == 0\n",
      "E    +  where 167 = len(['2mb_p_c', '2mba_c', '2mba_e', '2mpa_c', '2mpa_e', 'fe3pyovd_kt_e', ...])\n",
      "______________________________________________________________________________ test_metabolite_annotation_overview[bigg.metabolite] _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 147 metabolites (15.19%) lack annotation for\n",
      "E     bigg.metabolite:         aproa_c, id3acald_c, ind3ac_c, im4act_c,\n",
      "E     im4ac_c, ...\n",
      "E   assert 147 == 0\n",
      "E    +  where 147 = len(['aproa_c', 'id3acald_c', 'ind3ac_c', 'im4act_c', 'im4ac_c', 'imzacd_c', ...])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_overview[biocyc] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:153: in test_metabolite_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 301 metabolites (31.10%) lack annotation for biocyc:\n",
      "E     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\n",
      "E   assert 301 == 0\n",
      "E    +  where 301 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\n",
      "_____________________________________________________________________________________ test_reaction_annotation_overview[rhea] _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 744 reactions (56.49%) lack annotation for rhea:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 744 == 0\n",
      "E    +  where 744 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_overview[kegg.reaction] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 843 reactions (64.01%) lack annotation for\n",
      "E     kegg.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR160tipp,\n",
      "E     12DGR161tipp, 12DGR180tipp, ...\n",
      "E   assert 843 == 0\n",
      "E    +  where 843 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_overview[seed.reaction] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 450 reactions (34.17%) lack annotation for\n",
      "E     seed.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR160tipp,\n",
      "E     12DGR161tipp, 12DGR180tipp, ...\n",
      "E   assert 450 == 0\n",
      "E    +  where 450 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "______________________________________________________________________________ test_reaction_annotation_overview[metanetx.reaction] _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 224 reactions (17.01%) lack annotation for\n",
      "E     metanetx.reaction:         13PPDH2, 2AACLPPEAT160, 2MBAt6, 2MPAt6,\n",
      "E     2OBUT_Et, ...\n",
      "E   assert 224 == 0\n",
      "E    +  where 224 = len(['13PPDH2', '2AACLPPEAT160', '2MBAt6', '2MPAt6', '2OBUT_Et', '4HBAt', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_overview[bigg.reaction] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 134 reactions (10.17%) lack annotation for\n",
      "E     bigg.reaction:         AGPATr_BS, ALATA_D, ALATA_D2, ALATA_L2,\n",
      "E     ALCD22_L, ...\n",
      "E   assert 134 == 0\n",
      "E    +  where 134 = len(['AGPATr_BS', 'ALATA_D', 'ALATA_D2', 'ALATA_L2', 'ALCD22_L', 'CYSK2_I', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_overview[reactome] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 1132 reactions (85.95%) lack annotation for reactome:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 1132 == 0\n",
      "E    +  where 1132 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_overview[ec-code] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 620 reactions (47.08%) lack annotation for ec-code:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 620 == 0\n",
      "E    +  where 620 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "____________________________________________________________________________________ test_reaction_annotation_overview[brenda] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 1317 reactions (100.00%) lack annotation for brenda:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 1317 == 0\n",
      "E    +  where 1317 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "____________________________________________________________________________________ test_reaction_annotation_overview[biocyc] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:199: in test_reaction_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 730 reactions (55.43%) lack annotation for biocyc:\n",
      "E     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\n",
      "E     ...\n",
      "E   assert 730 == 0\n",
      "E    +  where 730 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_overview[refseq] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 10 genes (1.66%) lack annotation for refseq:\n",
      "E     spontaneous, WP_002838602_1, WP_012290557_1, FMG_RS06010, FMG_1297,\n",
      "E     ...\n",
      "E   assert 10 == 0\n",
      "E    +  where 10 = len(['spontaneous', 'WP_002838602_1', 'WP_012290557_1', 'FMG_RS06010', 'FMG_1297', 'FMG_0667', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_overview[uniprot] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 217 genes (36.11%) lack annotation for uniprot:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290371_1, ...\n",
      "E   assert 217 == 0\n",
      "E    +  where 217 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290371_1', 'spontaneous', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_overview[ecogene] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ecogene:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "________________________________________________________________________________ test_gene_product_annotation_overview[kegg.genes] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 10 genes (1.66%) lack annotation for kegg.genes:\n",
      "E     spontaneous, WP_002838602_1, WP_012290557_1, FMG_RS06010, FMG_1297,\n",
      "E     ...\n",
      "E   assert 10 == 0\n",
      "E    +  where 10 = len(['spontaneous', 'WP_002838602_1', 'WP_012290557_1', 'FMG_RS06010', 'FMG_1297', 'FMG_0667', ...])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_overview[ncbigi] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ncbigi:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_overview[ncbigene] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ncbigene:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_______________________________________________________________________________ test_gene_product_annotation_overview[ncbiprotein] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 217 genes (36.11%) lack annotation for ncbiprotein:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290371_1, ...\n",
      "E   assert 217 == 0\n",
      "E    +  where 217 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290371_1', 'spontaneous', ...])\n",
      "___________________________________________________________________________________ test_gene_product_annotation_overview[ccds] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for ccds:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "___________________________________________________________________________________ test_gene_product_annotation_overview[hprd] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for hprd:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "___________________________________________________________________________________ test_gene_product_annotation_overview[asap] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:245: in test_gene_product_annotation_overview\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: The following 601 genes (100.00%) lack annotation for asap:\n",
      "E     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\n",
      "E     WP_012290992_1, ...\n",
      "E   assert 601 == 0\n",
      "E    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_____________________________________________________________________________ test_metabolite_annotation_wrong_ids[pubchem.compound] ______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:281: in test_metabolite_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no metabolite annotations for the pubchem.compound database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "_______________________________________________________________________________ test_metabolite_annotation_wrong_ids[seed.compound] _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:292: in test_metabolite_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 1 metabolite annotations (0.14%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the\n",
      "E     seed.compound         database: trdox_c\n",
      "E   assert 1 == 0\n",
      "E    +  where 1 = len(['trdox_c'])\n",
      "___________________________________________________________________________________ test_metabolite_annotation_wrong_ids[inchi] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:281: in test_metabolite_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no metabolite annotations for the inchi database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "____________________________________________________________________________________ test_reaction_annotation_wrong_ids[rhea] _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 59 reaction annotations (4.48%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the rhea\n",
      "E     database: AEPabcpp, ARGabc, ASPabc, ASPabcpp, CA2abc, ...\n",
      "E   assert 59 == 0\n",
      "E    +  where 59 = len(['AEPabcpp', 'ARGabc', 'ASPabc', 'ASPabcpp', 'CA2abc', 'CA2abc1', ...])\n",
      "________________________________________________________________________________ test_reaction_annotation_wrong_ids[kegg.reaction] ________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 12 reaction annotations (0.91%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the\n",
      "E     kegg.reaction         database: AMALT1, AMALT2, AMALT3, HCO3E, LACZpp,\n",
      "E     ...\n",
      "E   assert 12 == 0\n",
      "E    +  where 12 = len(['AMALT1', 'AMALT2', 'AMALT3', 'HCO3E', 'LACZpp', 'MAL6PG', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_wrong_ids[ec-code] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 77 reaction annotations (5.85%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the ec-code\n",
      "E     database: 4ABUTD, 4HTHRS, AKGDH, AKGt2r, ALCD4, ...\n",
      "E   assert 77 == 0\n",
      "E    +  where 77 = len(['4ABUTD', '4HTHRS', 'AKGDH', 'AKGt2r', 'ALCD4', 'ALCD4y', ...])\n",
      "___________________________________________________________________________________ test_reaction_annotation_wrong_ids[brenda] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:328: in test_reaction_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no reaction annotations for the brenda database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "___________________________________________________________________________________ test_reaction_annotation_wrong_ids[biocyc] ____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:339: in test_reaction_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 5 reaction annotations (0.38%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the biocyc\n",
      "E     database: PHETYRr, TYRALAr, TYRGLUr, TYRTHRr, GLYTYRAP\n",
      "E   assert 5 == 0\n",
      "E    +  where 5 = len(['PHETYRr', 'TYRALAr', 'TYRGLUr', 'TYRTHRr', 'GLYTYRAP'])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_wrong_ids[refseq] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:386: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\n",
      "E   AssertionError: A total of 591 gene annotations (98.34%) do not match the\n",
      "E     regular expression patterns defined on identifiers.org for the refseq\n",
      "E     database: WP_012290939_1, WP_012290272_1, WP_002842355_1,\n",
      "E     WP_012291190_1, WP_012290992_1, ...\n",
      "E   assert 591 == 0\n",
      "E    +  where 591 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ecogene] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ecogene database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "_________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ncbigi] __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ncbigi database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ncbigene] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ncbigene database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_wrong_ids[ccds] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the ccds database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_wrong_ids[hprd] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the hprd database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "__________________________________________________________________________________ test_gene_product_annotation_wrong_ids[asap] ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py:375: in test_gene_product_annotation_wrong_ids\n",
      "    assert len(total) > 0, ann[\"message\"][db]\n",
      "E   AssertionError: There are no gene annotations for the asap database.\n",
      "E   assert 0 > 0\n",
      "E    +  where 0 = len([])\n",
      "____________________________________________________________________________________ test_gene_protein_reaction_rule_presence _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:206: in test_gene_protein_reaction_rule_presence\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: There are a total of 305 reactions (23.16%) without GPR:\n",
      "E     PAPA181pp, 2AGPE161tipp, NTR3B, BUTCT, SPT_syn, ...\n",
      "E   assert 305 == 0\n",
      "E    +  where 305 = len(['PAPA181pp', '2AGPE161tipp', 'NTR3B', 'BUTCT', 'SPT_syn', 'DAPDC', ...])\n",
      "______________________________________________________________________________________ test_transport_reaction_gpr_presence _______________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:499: in test_transport_reaction_gpr_presence\n",
      "    assert ann[\"metric\"] < 0.2, ann[\"message\"]\n",
      "E   AssertionError: There are a total of 106 transport reactions (31.27% of all\n",
      "E     transport reactions) without GPR:         SELTt, TMAMt, SELt,\n",
      "E     PACALDtex, ARBT6Pt, ...\n",
      "E   assert 0.31268436578171094 < 0.2\n",
      "__________________________________________________________________________________________ test_find_unique_metabolites ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:555: in test_find_unique_metabolites\n",
      "    assert len(ann[\"data\"]) < len(model.metabolites), ann[\"message\"]\n",
      "E   AssertionError: Not counting the same entities in other compartments, there is a\n",
      "E     total of 968 (100.00%) unique metabolites in the model: dad_2_c,\n",
      "E     drib_c, dpcoa_e, 5mtr_c, gthrd_e, ...\n",
      "E   assert 968 < 968\n",
      "E    +  where 968 = len(['dad_2_c', 'drib_c', 'dpcoa_e', '5mtr_c', 'gthrd_e', 'glcn_c', ...])\n",
      "E    +  and   968 = len([<Metabolite 10fthf_c at 0x7ff0541a2df0>, <Metabolite 12dag3p_BS_c at 0x7ff0541a2e80>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff054124790>, <Metabolite tyrthr_c at 0x7ff0541247c0>, <Metabolite gly_tyr_c at 0x7ff0541247f0>])\n",
      "E    +    where [<Metabolite 10fthf_c at 0x7ff0541a2df0>, <Metabolite 12dag3p_BS_c at 0x7ff0541a2e80>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff054124790>, <Metabolite tyrthr_c at 0x7ff0541247c0>, <Metabolite gly_tyr_c at 0x7ff0541247f0>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff0542059a0>.metabolites\n",
      "_________________________________________________________________________________ test_find_duplicate_metabolites_in_compartments _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:584: in test_find_duplicate_metabolites_in_compartments\n",
      "    len(ann[\"data\"]), truncate(ann[\"data\"])))\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/utils.py:170: in truncate\n",
      "    return \", \".join(sequence)\n",
      "E   TypeError: sequence item 0: expected str instance, tuple found\n",
      "____________________________________________________________________________ test_find_reactions_with_partially_identical_annotations _____________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:624: in test_find_reactions_with_partially_identical_annotations\n",
      "    assert total == 0, ann[\"message\"]\n",
      "E   AssertionError: Based on annotations there are 137 different groups of overlapping\n",
      "E     annotation which corresponds to a total of 312 duplicated reactions in\n",
      "E     the model.\n",
      "E   assert 312 == 0\n",
      "__________________________________________________________________________________________ test_find_duplicate_reactions __________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:660: in test_find_duplicate_reactions\n",
      "    {}\"\"\".format(num, truncate(duplicates)))\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/utils.py:168: in truncate\n",
      "    return \", \".join(sequence[:LIST_SLICE] + [\"...\"])\n",
      "E   TypeError: sequence item 0: expected str instance, tuple found\n",
      "____________________________________________________________________________________ test_find_reactions_with_identical_genes _____________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:692: in test_find_reactions_with_identical_genes\n",
      "    assert num_dup == 0, ann[\"message\"]\n",
      "E   AssertionError: Based only on equal genes there are 154 different groups of\n",
      "E     identical reactions which corresponds to a total of 601\n",
      "E     duplicated reactions in the model.\n",
      "E   assert 601 == 0\n",
      "__________________________________________________________________________________________ test_find_medium_metabolites ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py:713: in test_find_medium_metabolites\n",
      "    ann[\"metric\"] = len(ann[\"data\"]) / num_ex\n",
      "E   TypeError: unsupported operand type(s) for /: 'int' and 'list'\n",
      "________________________________________________________________________________________ test_biomass_consistency[Growth] _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py:121: in test_biomass_consistency\n",
      "    assert outcome, ann[\"message\"][reaction_id]\n",
      "E   AssertionError: The component molar mass of the biomass reaction Growth sums up to\n",
      "E     1.0300277967729958             which is outside of the 1e-03 margin\n",
      "E     from 1 mmol / g[CDW] / h.\n",
      "E   assert False\n",
      "________________________________________________________________________________________ test_fast_growth_default[Growth] _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py:370: in test_fast_growth_default\n",
      "    assert outcome, ann[\"message\"][reaction_id]\n",
      "E   AssertionError: Using the biomass reaction Growth and when the model is simulated on\n",
      "E     the provided default medium the growth rate is *lower* than that\n",
      "E     of the fastest bacteria. This is to be expected for             a\n",
      "E     majority of organisms.\n",
      "E   assert False\n",
      "________________________________________________________________________________ test_essential_precursors_not_in_biomass[Growth] _________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py:494: in test_essential_precursors_not_in_biomass\n",
      "    assert len(ann[\"data\"][reaction_id]) == 0, ann[\"message\"][reaction_id]\n",
      "E   AssertionError: Growth lacks a total of 1 essential metabolites         (1.72% of all\n",
      "E     biomass precursors). Specifically         these are: ['fmn_c'].\n",
      "E   assert 1 == 0\n",
      "E    +  where 1 = len(['fmn_c'])\n",
      "__________________________________________________________________________________________ test_reaction_charge_balance ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:158: in test_reaction_charge_balance\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 3 (0.26%) reactions are charge unbalanced with at\n",
      "E     least one of the metabolites not having a charge or the overall\n",
      "E     charge not equal to 0: BTS2, AGPATr_BS, G3POA_BS\n",
      "E   assert 3 == 0\n",
      "E    +  where 3 = len(['BTS2', 'AGPATr_BS', 'G3POA_BS'])\n",
      "___________________________________________________________________________________________ test_reaction_mass_balance ____________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:193: in test_reaction_mass_balance\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 2 (0.17%) reactions are mass unbalanced with at least\n",
      "E     one of the metabolites not having a formula or the overall mass not\n",
      "E     equal to 0: AGPATr_BS, G3POA_BS\n",
      "E   assert 2 == 0\n",
      "E    +  where 2 = len(['AGPATr_BS', 'G3POA_BS'])\n",
      "_____________________________________________________________________________________________ test_blocked_reactions ______________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:222: in test_blocked_reactions\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: There are 98 (7.44%) blocked reactions in         the model: EX_btn_e,\n",
      "E     EX_chol_e, EX_rmn_e, EX_spmd_e, EX_xyl__D_e, ...\n",
      "E   assert 98 == 0\n",
      "E    +  where 98 = len(['EX_btn_e', 'EX_chol_e', 'EX_rmn_e', 'EX_spmd_e', 'EX_xyl__D_e', 'ALDD22x', ...])\n",
      "__________________________________________________________________________________ test_find_stoichiometrically_balanced_cycles ___________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:246: in test_find_stoichiometrically_balanced_cycles\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: There are 111 (8.43%) reactions         which participate in SBC in\n",
      "E     the model: 13PPDH, 13PPDH2, 4ABUTD, ABUTD, ACCOAL, ...\n",
      "E   assert 111 == 0\n",
      "E    +  where 111 = len(['13PPDH', '13PPDH2', '4ABUTD', 'ABUTD', 'ACCOAL', 'ACKr', ...])\n",
      "________________________________________________________________________________________________ test_find_orphans ________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:271: in test_find_orphans\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 42 (4.34%) metabolites are not produced by any reaction\n",
      "E     of the model: cl_p, inost_c, aproa_c, id3acald_c, im4act_c, ...\n",
      "E   assert 42 == 0\n",
      "E    +  where 42 = len(['cl_p', 'inost_c', 'aproa_c', 'id3acald_c', 'im4act_c', 'imzacd_c', ...])\n",
      "_______________________________________________________________________________________________ test_find_deadends ________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:295: in test_find_deadends\n",
      "    assert ann[\"data\"] == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 45 (4.65%) metabolites are not consumed by any reaction\n",
      "E     of the model: 2ins_c, spmd_c, ind3ac_c, im4ac_c, imzac_c, ...\n",
      "E   assert ['2ins_c', 'spmd_c', 'ind3ac_c', 'im4ac_c', 'imzac_c', '4aabutn_c', ...] == 0\n",
      "_____________________________________________________________________________________________ test_find_disconnected ______________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:319: in test_find_disconnected\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 5 (0.52%) metabolites are not associated with any\n",
      "E     reaction of the model: 3php_c, pa160140_c, pa160180_c, pa160205n3_c,\n",
      "E     pa160226n3_c\n",
      "E   assert 5 == 0\n",
      "E    +  where 5 = len(['3php_c', 'pa160140_c', 'pa160180_c', 'pa160205n3_c', 'pa160226n3_c'])\n",
      "_______________________________________________________________________________ test_find_metabolites_not_produced_with_open_bounds _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:349: in test_find_metabolites_not_produced_with_open_bounds\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 250 (25.83%) metabolites cannot be produced in complete\n",
      "E     medium: 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr161_c,\n",
      "E     ...\n",
      "E   assert 250 == 0\n",
      "E    +  where 250 = len(['12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr161_c', '12dgr161_p', ...])\n",
      "_______________________________________________________________________________ test_find_metabolites_not_consumed_with_open_bounds _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:379: in test_find_metabolites_not_consumed_with_open_bounds\n",
      "    assert len(ann[\"data\"]) == 0, ann[\"message\"]\n",
      "E   AssertionError: A total of 255 (26.34%) metabolites cannot be consumed in complete\n",
      "E     medium: 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr161_c,\n",
      "E     ...\n",
      "E   assert 255 == 0\n",
      "E    +  where 255 = len(['12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr161_c', '12dgr161_p', ...])\n",
      "______________________________________________________________________________ test_find_reactions_unbounded_flux_default_condition _______________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py:413: in test_find_reactions_unbounded_flux_default_condition\n",
      "    assert ann[\"metric\"] <= 0.1, ann[\"message\"]\n",
      "E   AssertionError:  A fraction of 22.32% of the non-blocked reactions (in total 98\n",
      "E     reactions) can carry unbounded flux in the default model\n",
      "E     condition. Unbounded reactions may be involved in\n",
      "E     thermodynamically infeasible cycles: 13PPDH, 13PPDH2, 4ABUTD, ABUTD,\n",
      "E     ACCOAL, ...\n",
      "E   assert 0.22323462414578588 <= 0.1\n",
      "_________________________________________________________________________________________________ test_sbml_level _________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py:39: in test_sbml_level\n",
      "    sbml_version[0], sbml_version[1])\n",
      "E   TypeError: 'NoneType' object is not subscriptable\n",
      "________________________________________________________________________________________________ test_fbc_presence ________________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py:66: in test_fbc_presence\n",
      "    fbc_present = sbml_version[2] is not None\n",
      "E   TypeError: 'NoneType' object is not subscriptable\n",
      "__________________________________________________________________________________________ test_metabolite_sbo_presence ___________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:58: in test_metabolite_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.metabolites), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 metabolites (0.00%) lack annotation with any type\n",
      "E     of SBO term:\n",
      "E   assert 0 == 968\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   968 = len([<Metabolite 10fthf_c at 0x7ff0541a2df0>, <Metabolite 12dag3p_BS_c at 0x7ff0541a2e80>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff054124790>, <Metabolite tyrthr_c at 0x7ff0541247c0>, <Metabolite gly_tyr_c at 0x7ff0541247f0>])\n",
      "E    +    where [<Metabolite 10fthf_c at 0x7ff0541a2df0>, <Metabolite 12dag3p_BS_c at 0x7ff0541a2e80>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff054124790>, <Metabolite tyrthr_c at 0x7ff0541247c0>, <Metabolite gly_tyr_c at 0x7ff0541247f0>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff0542059a0>.metabolites\n",
      "___________________________________________________________________________________________ test_reaction_sbo_presence ____________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:88: in test_reaction_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.reactions), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 reactions (0.00%) lack annotation with any type\n",
      "E     of SBO term:\n",
      "E   assert 0 == 1317\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   1317 = len([<Reaction 12DGR120tipp at 0x7ff0540d9fa0>, <Reaction 12DGR140tipp at 0x7ff05402e2e0>, <Reaction 12DGR160tipp at 0x7ff...ff045ed5df0>, <Reaction KAS8 at 0x7ff045ed5bb0>, <Reaction NNDPR at 0x7ff045ed5fa0>, <Reaction PPND at 0x7ff045ed5eb0>])\n",
      "E    +    where [<Reaction 12DGR120tipp at 0x7ff0540d9fa0>, <Reaction 12DGR140tipp at 0x7ff05402e2e0>, <Reaction 12DGR160tipp at 0x7ff...ff045ed5df0>, <Reaction KAS8 at 0x7ff045ed5bb0>, <Reaction NNDPR at 0x7ff045ed5fa0>, <Reaction PPND at 0x7ff045ed5eb0>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff0542059a0>.reactions\n",
      "_____________________________________________________________________________________________ test_gene_sbo_presence ______________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:117: in test_gene_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.genes), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 genes (0.00%) lack annotation with any type of\n",
      "E     SBO term:\n",
      "E   assert 0 == 601\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   601 = len([<Gene WP_012290939_1 at 0x7ff0540d9f70>, <Gene WP_012290272_1 at 0x7ff0541a2d00>, <Gene WP_002842355_1 at 0x7ff0540d9...7ff05402e190>, <Gene FMG_0827 at 0x7ff05402e160>, <Gene FMG_1032 at 0x7ff05402e130>, <Gene FMG_0500 at 0x7ff05402e100>])\n",
      "E    +    where [<Gene WP_012290939_1 at 0x7ff0540d9f70>, <Gene WP_012290272_1 at 0x7ff0541a2d00>, <Gene WP_002842355_1 at 0x7ff0540d9...7ff05402e190>, <Gene FMG_0827 at 0x7ff05402e160>, <Gene FMG_1032 at 0x7ff05402e130>, <Gene FMG_0500 at 0x7ff05402e100>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff0542059a0>.genes\n",
      "__________________________________________________________________________________ test_metabolic_reaction_specific_sbo_presence __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:150: in test_metabolic_reaction_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(pure), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 metabolic reactions (0.00% of all purely\n",
      "E     metabolic reactions) lack annotation with the SBO term\n",
      "E     \"SBO:0000176\" for 'biochemical reaction':\n",
      "E   assert 0 == 818\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   818 = len({<Reaction FACOAL170_anteiso at 0x7ff04663adc0>, <Reaction CYTOM at 0x7ff046707fd0>, <Reaction FACOAL170_ISO at 0x7ff0...>, <Reaction CLPNH180pp at 0x7ff04675ffa0>, <Reaction FBP at 0x7ff04663ae20>, <Reaction GDPDPK at 0x7ff0466384c0>, ...})\n",
      "__________________________________________________________________________________ test_transport_reaction_specific_sbo_presence __________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:188: in test_transport_reaction_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(transports), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 metabolic reactions (0.00% of all transport\n",
      "E     reactions) lack annotation with one of the SBO terms: ['SBO:0000185',\n",
      "E     'SBO:0000588', 'SBO:0000587', 'SBO:0000655', 'SBO:0000654',\n",
      "E     'SBO:0000660', 'SBO:0000659', 'SBO:0000657', 'SBO:0000658'] for\n",
      "E     'biochemical reaction':\n",
      "E   assert 0 == 339\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   339 = len({<Reaction SELTt at 0x7ff046238340>, <Reaction DIPEPabc3 at 0x7ff0466d85e0>, <Reaction PA180abcpp at 0x7ff0463a0820>, <Reaction GLCNt2r at 0x7ff046638820>, <Reaction NIabc at 0x7ff046420880>, <Reaction TMAMt at 0x7ff046198a30>, ...})\n",
      "______________________________________________________________________________________ test_metabolite_specific_sbo_presence ______________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:218: in test_metabolite_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.metabolites), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 transport reactions (0.00% of all metabolites)\n",
      "E     lack annotation with the SBO term \"SBO:0000247\" for\n",
      "E     'simple chemical':\n",
      "E   assert 0 == 968\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   968 = len([<Metabolite 10fthf_c at 0x7ff0541a2df0>, <Metabolite 12dag3p_BS_c at 0x7ff0541a2e80>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff054124790>, <Metabolite tyrthr_c at 0x7ff0541247c0>, <Metabolite gly_tyr_c at 0x7ff0541247f0>])\n",
      "E    +    where [<Metabolite 10fthf_c at 0x7ff0541a2df0>, <Metabolite 12dag3p_BS_c at 0x7ff0541a2e80>, <Metabolite 12dgr120_c at 0x7ff...abolite tyrglu_c at 0x7ff054124790>, <Metabolite tyrthr_c at 0x7ff0541247c0>, <Metabolite gly_tyr_c at 0x7ff0541247f0>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff0542059a0>.metabolites\n",
      "_________________________________________________________________________________________ test_gene_specific_sbo_presence _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:248: in test_gene_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(model.genes), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 genes (0.00% of all genes) lack             annotation\n",
      "E     with the SBO term \"SBO:0000243\" for             'gene':\n",
      "E   assert 0 == 601\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   601 = len([<Gene WP_012290939_1 at 0x7ff0540d9f70>, <Gene WP_012290272_1 at 0x7ff0541a2d00>, <Gene WP_002842355_1 at 0x7ff0540d9...7ff05402e190>, <Gene FMG_0827 at 0x7ff05402e160>, <Gene FMG_1032 at 0x7ff05402e130>, <Gene FMG_0500 at 0x7ff05402e100>])\n",
      "E    +    where [<Gene WP_012290939_1 at 0x7ff0540d9f70>, <Gene WP_012290272_1 at 0x7ff0541a2d00>, <Gene WP_002842355_1 at 0x7ff0540d9...7ff05402e190>, <Gene FMG_0827 at 0x7ff05402e160>, <Gene FMG_1032 at 0x7ff05402e130>, <Gene FMG_0500 at 0x7ff05402e100>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7ff0542059a0>.genes\n",
      "_______________________________________________________________________________________ test_exchange_specific_sbo_presence _______________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:290: in test_exchange_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(exchanges), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 exchange reactions (0.00% of all exchange\n",
      "E     reactions) lack annotation with the SBO term \"SBO:0000627\" for\n",
      "E     'exchange reaction':\n",
      "E   assert 0 == 157\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   157 = len([<Reaction EX_14glucan_e at 0x7ff0460dafd0>, <Reaction EX_15dap_e at 0x7ff0460da6a0>, <Reaction EX_26dap__M_e at 0x7ff...Reaction EX_atp_e at 0x7ff045f77820>, <Reaction EX_pan4p_e at 0x7ff045f77790>, <Reaction EX_dpcoa_e at 0x7ff045f77df0>])\n",
      "_________________________________________________________________________________________ test_sink_specific_sbo_presence _________________________________________________________________________________________\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py:376: in test_sink_specific_sbo_presence\n",
      "    assert len(ann[\"data\"]) == len(sinks), ann[\"message\"]\n",
      "E   AssertionError: A total of 0 genes (0.00% of all sink reactions) lack\n",
      "E     annotation with the SBO term \"SBO:0000632\" for         'sink\n",
      "E     reaction':\n",
      "E   assert 0 == 2\n",
      "E    +  where 0 = len([])\n",
      "E    +  and   2 = len([<Reaction sink_lipopb_c at 0x7ff0460daf70>, <Reaction sink_mobd_c at 0x7ff0460dac10>])\n",
      "================================================================================================ warnings summary =================================================================================================\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/_pytest/config/__init__.py:886\n",
      "  /home/salatan/anaconda3/lib/python3.8/site-packages/_pytest/config/__init__.py:886: PytestAssertRewriteWarning: Module already imported so cannot be rewritten: anyio\n",
      "    self._mark_plugins_for_rewrite(hook)\n",
      "\n",
      "-- Docs: https://docs.pytest.org/en/latest/warnings.html\n",
      "========================================================================== 77 failed, 49 passed, 19 skipped, 1 warnings in 19.81 seconds ==========================================================================\n"
     ]
    }
   ],
   "source": [
    "model = cobra.io.read_sbml_model(\"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.xml\")\n",
    "# Make memote report\n",
    "result = memote.test_model(model, results=True)  #, skip=[\"test_find_metabolites_not_produced_with_open_bounds\"])\n",
    "report = memote.snapshot_report(result[1], config=None, html=True)\n",
    "with open(\"2.2/memote-reports/report.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.html\", \"w\") as handle:\n",
    "    handle.write(report)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "bb38197d-9c76-4567-9982-52a44d6518d4",
   "metadata": {},
   "source": [
    "### Clean Up annotations via own python code:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "ac0395fb-708c-4521-8d7e-74ebfe10e1a2",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Model polishing via ModelPolisher\n",
    "# cd ModelPolisher\n",
    "# systemctl start docker\n",
    "# sudo docker-compose run -v /mnt/Data/Uni/7.Semester/Nextcloud_SysBio_Linux/Josua_Carl_BT/finegoldia_magna_py/2.2:/models/ polisher java -jar /ModelPolisher-2.1-beta.jar --input=/models/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.xml --output=/models/mp-output/finegoldia_magna_ATCC_29328_2.2.mp2.xml  --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "cfa0a546-0e89-4579-9806-03f89cb15201",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "100%|████████████████████████████████████| 14684/14684 [00:25<00:00, 569.91it/s]\n"
     ]
    }
   ],
   "source": [
    "!python annotate_links_from_mp.py \"2.2/mp-output2/model.xml\" \"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.xml\" \"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.mp2.xml\" \"finegoldia_magna\" \"2.2\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "e42277d7-1afa-4ff1-a5a6-a35b1de8cae4",
   "metadata": {
    "collapsed": true,
    "jupyter": {
     "outputs_hidden": true
    },
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "100%|██████████████████████████████████████| 1317/1317 [00:03<00:00, 425.95it/s]\n",
      "100%|███████████████████████████████████████| 1317/1317 [04:44<00:00,  4.62it/s]\n",
      "\u001b[1m============================= test session starts ==============================\u001b[0m\n",
      "platform linux -- Python 3.8.8, pytest-4.6.11, py-1.10.0, pluggy-0.13.1\n",
      "rootdir: /home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests\n",
      "plugins: anyio-3.3.0\n",
      "collected 145 items                                                            \u001b[0m\u001b[1m\n",
      "\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py \u001b[32m.\u001b[0m\u001b[36m [  0%]\n",
      "\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[36m         [ 44%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py \u001b[32m.\u001b[0m\u001b[36m [ 45%]\n",
      "\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[36m                                                   [ 60%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py \u001b[32m.\u001b[0m\u001b[36m [ 61%]\n",
      "\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[31mF\u001b[0m\u001b[36m                                                                [ 67%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py \u001b[32m.\u001b[0m\u001b[36m [ 68%]\n",
      "\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[33ms\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[36m                                               [ 86%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_essentiality.py \u001b[33ms\u001b[0m\u001b[36m [ 86%]\n",
      "\u001b[0m\u001b[36m                                                                         [ 86%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_growth.py \u001b[33ms\u001b[0m\u001b[36m [ 87%]\n",
      "\u001b[0m\u001b[36m                                                                         [ 87%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_matrix.py \u001b[32m.\u001b[0m\u001b[36m [ 88%]\n",
      "\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[32m.\u001b[0m\u001b[36m                                                                      [ 90%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py \u001b[31mF\u001b[0m\u001b[36m [ 91%]\n",
      "\u001b[0m\u001b[31mF\u001b[0m\u001b[36m                                                                        [ 91%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py \u001b[31mF\u001b[0m\u001b[36m [ 92%]\n",
      "\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[31mF\u001b[0m\u001b[33ms\u001b[0m\u001b[31mF\u001b[0m\u001b[32m.\u001b[0m\u001b[36m                                                               [ 99%]\u001b[0m\n",
      "../../../../../../../home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_thermodynamics.py \u001b[32m.\u001b[0m\u001b[36m [100%]\u001b[0m\n",
      "\n",
      "=================================== FAILURES ===================================\n",
      "\u001b[31m\u001b[1m____________ test_metabolite_annotation_overview[pubchem.compound] _____________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 968 metabolites (100.00%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     pubchem.compound:         10fthf_c, 12dag3p_BS_c, 12dgr120_c,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dgr120_p, 12dgr140_c, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 968 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 968 = len(['10fthf_c', '12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m______________ test_metabolite_annotation_overview[kegg.compound] ______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 359 metabolites (37.09%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     kegg.compound:         12dag3p_BS_c, 12dgr120_c, 12dgr120_p,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dgr140_c, 12dgr140_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 359 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 359 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m______________ test_metabolite_annotation_overview[seed.compound] ______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 248 metabolites (25.62%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     seed.compound:         12dag3p_BS_c, 12dgr120_c, 12dgr120_p,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dgr140_c, 12dgr140_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 248 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 248 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_metabolite_annotation_overview[inchikey] _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 295 metabolites (30.48%) lack annotation for inchikey:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 295 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 295 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_metabolite_annotation_overview[inchi] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 968 metabolites (100.00%) lack annotation for inchi:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     10fthf_c, 12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 968 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 968 = len(['10fthf_c', '12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_metabolite_annotation_overview[chebi] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 315 metabolites (32.54%) lack annotation for chebi:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 315 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 315 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_metabolite_annotation_overview[hmdb] ___________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 424 metabolites (43.80%) lack annotation for hmdb:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 424 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 424 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_metabolite_annotation_overview[reactome] _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 589 metabolites (60.85%) lack annotation for reactome:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 589 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 589 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m____________ test_metabolite_annotation_overview[metanetx.chemical] ____________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 167 metabolites (17.25%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     metanetx.chemical:         2mb_p_c, 2mba_c, 2mba_e, 2mpa_c, 2mpa_e,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 167 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 167 = len(['2mb_p_c', '2mba_c', '2mba_e', '2mpa_c', '2mpa_e', 'fe3pyovd_kt_e', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________ test_metabolite_annotation_overview[bigg.metabolite] _____________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 147 metabolites (15.19%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     bigg.metabolite:         aproa_c, id3acald_c, ind3ac_c, im4act_c,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     im4ac_c, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 147 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 147 = len(['aproa_c', 'id3acald_c', 'ind3ac_c', 'im4act_c', 'im4ac_c', 'imzacd_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_metabolite_annotation_overview[biocyc] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:153: in test_metabolite_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 301 metabolites (31.10%) lack annotation for biocyc:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12dag3p_BS_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 301 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 301 = len(['12dag3p_BS_c', '12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr160_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m___________________ test_reaction_annotation_overview[rhea] ____________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 737 reactions (55.96%) lack annotation for rhea:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 737 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 737 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_reaction_annotation_overview[kegg.reaction] _______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 842 reactions (63.93%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     kegg.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR160tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12DGR161tipp, 12DGR180tipp, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 842 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 842 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_reaction_annotation_overview[seed.reaction] _______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 445 reactions (33.79%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     seed.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR160tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12DGR161tipp, 12DGR180tipp, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 445 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 445 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________ test_reaction_annotation_overview[metanetx.reaction] _____________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 196 reactions (14.88%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     metanetx.reaction:         13PPDH2, 2AACLPPEAT160, 2MBAt6, 2MPAt6,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     2OBUT_Et, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 196 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 196 = len(['13PPDH2', '2AACLPPEAT160', '2MBAt6', '2MPAt6', '2OBUT_Et', '4HBAt', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_reaction_annotation_overview[bigg.reaction] _______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 134 reactions (10.17%) lack annotation for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     bigg.reaction:         AGPATr_BS, ALATA_D, ALATA_D2, ALATA_L2,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ALCD22_L, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 134 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 134 = len(['AGPATr_BS', 'ALATA_D', 'ALATA_D2', 'ALATA_L2', 'ALCD22_L', 'CYSK2_I', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_reaction_annotation_overview[reactome] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 1129 reactions (85.73%) lack annotation for reactome:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 1129 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 1129 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_reaction_annotation_overview[ec-code] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 619 reactions (47.00%) lack annotation for ec-code:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 619 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 619 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_reaction_annotation_overview[brenda] ___________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 1317 reactions (100.00%) lack annotation for brenda:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 1317 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 1317 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_reaction_annotation_overview[biocyc] ___________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:199: in test_reaction_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 726 reactions (55.13%) lack annotation for biocyc:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     12DGR120tipp, 12DGR140tipp, 12DGR160tipp, 12DGR161tipp, 12DGR180tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 726 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 726 = len(['12DGR120tipp', '12DGR140tipp', '12DGR160tipp', '12DGR161tipp', '12DGR180tipp', '12DGR181tipp', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_gene_product_annotation_overview[refseq] _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 10 genes (1.66%) lack annotation for refseq:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     spontaneous, WP_002838602_1, WP_012290557_1, FMG_RS06010, FMG_1297,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 10 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 10 = len(['spontaneous', 'WP_002838602_1', 'WP_012290557_1', 'FMG_RS06010', 'FMG_1297', 'FMG_0667', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_gene_product_annotation_overview[uniprot] ________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 217 genes (36.11%) lack annotation for uniprot:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290371_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 217 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 217 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290371_1', 'spontaneous', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_gene_product_annotation_overview[ecogene] ________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 601 genes (100.00%) lack annotation for ecogene:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290992_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 601 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m______________ test_gene_product_annotation_overview[kegg.genes] _______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 10 genes (1.66%) lack annotation for kegg.genes:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     spontaneous, WP_002838602_1, WP_012290557_1, FMG_RS06010, FMG_1297,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 10 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 10 = len(['spontaneous', 'WP_002838602_1', 'WP_012290557_1', 'FMG_RS06010', 'FMG_1297', 'FMG_0667', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_gene_product_annotation_overview[ncbigi] _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 601 genes (100.00%) lack annotation for ncbigi:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290992_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 601 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_gene_product_annotation_overview[ncbigene] ________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 601 genes (100.00%) lack annotation for ncbigene:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290992_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 601 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m______________ test_gene_product_annotation_overview[ncbiprotein] ______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 217 genes (36.11%) lack annotation for ncbiprotein:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290371_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 217 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 217 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290371_1', 'spontaneous', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_gene_product_annotation_overview[ccds] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 601 genes (100.00%) lack annotation for ccds:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290992_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 601 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_gene_product_annotation_overview[hprd] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 601 genes (100.00%) lack annotation for hprd:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290992_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 601 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_gene_product_annotation_overview[asap] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:245: in test_gene_product_annotation_overview\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The following 601 genes (100.00%) lack annotation for asap:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290939_1, WP_012290272_1, WP_002842355_1, WP_012291190_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012290992_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 601 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 601 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m____________ test_metabolite_annotation_wrong_ids[pubchem.compound] ____________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:281: in test_metabolite_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no metabolite annotations for the pubchem.compound database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________ test_metabolite_annotation_wrong_ids[seed.compound] ______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:292: in test_metabolite_annotation_wrong_ids\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 1 metabolite annotations (0.14%) do not match the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     regular expression patterns defined on identifiers.org for the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     seed.compound         database: trdox_c\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 1 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 1 = len(['trdox_c'])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_metabolite_annotation_wrong_ids[inchi] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:281: in test_metabolite_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no metabolite annotations for the inchi database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m___________________ test_reaction_annotation_wrong_ids[rhea] ___________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:339: in test_reaction_annotation_wrong_ids\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 59 reaction annotations (4.48%) do not match the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     regular expression patterns defined on identifiers.org for the rhea\u001b[0m\n",
      "\u001b[1m\u001b[31mE     database: AEPabcpp, ARGabc, ASPabc, ASPabcpp, CA2abc, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 59 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 59 = len(['AEPabcpp', 'ARGabc', 'ASPabc', 'ASPabcpp', 'CA2abc', 'CA2abc1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m______________ test_reaction_annotation_wrong_ids[kegg.reaction] _______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:339: in test_reaction_annotation_wrong_ids\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 12 reaction annotations (0.91%) do not match the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     regular expression patterns defined on identifiers.org for the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     kegg.reaction         database: AMALT1, AMALT2, AMALT3, HCO3E, LACZpp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 12 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 12 = len(['AMALT1', 'AMALT2', 'AMALT3', 'HCO3E', 'LACZpp', 'MAL6PG', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_reaction_annotation_wrong_ids[ec-code] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:339: in test_reaction_annotation_wrong_ids\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 79 reaction annotations (6.00%) do not match the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     regular expression patterns defined on identifiers.org for the ec-code\u001b[0m\n",
      "\u001b[1m\u001b[31mE     database: 4ABUTD, 4HTHRS, AKGDH, AKGt2r, ALCD4, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 79 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 79 = len(['4ABUTD', '4HTHRS', 'AKGDH', 'AKGt2r', 'ALCD4', 'ALCD4y', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_reaction_annotation_wrong_ids[brenda] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:328: in test_reaction_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no reaction annotations for the brenda database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________ test_reaction_annotation_wrong_ids[biocyc] __________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:339: in test_reaction_annotation_wrong_ids\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 5 reaction annotations (0.38%) do not match the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     regular expression patterns defined on identifiers.org for the biocyc\u001b[0m\n",
      "\u001b[1m\u001b[31mE     database: PHETYRr, TYRALAr, TYRGLUr, TYRTHRr, GLYTYRAP\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 5 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 5 = len(['PHETYRr', 'TYRALAr', 'TYRGLUr', 'TYRTHRr', 'GLYTYRAP'])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_gene_product_annotation_wrong_ids[refseq] ________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:386: in test_gene_product_annotation_wrong_ids\n",
      "\u001b[1m    assert len(ann[\"data\"][db]) == 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 591 gene annotations (98.34%) do not match the\u001b[0m\n",
      "\u001b[1m\u001b[31mE     regular expression patterns defined on identifiers.org for the refseq\u001b[0m\n",
      "\u001b[1m\u001b[31mE     database: WP_012290939_1, WP_012290272_1, WP_002842355_1,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     WP_012291190_1, WP_012290992_1, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 591 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 591 = len(['WP_012290939_1', 'WP_012290272_1', 'WP_002842355_1', 'WP_012291190_1', 'WP_012290992_1', 'WP_012290328_1', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_gene_product_annotation_wrong_ids[ecogene] ________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:375: in test_gene_product_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no gene annotations for the ecogene database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_gene_product_annotation_wrong_ids[ncbigi] ________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:375: in test_gene_product_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no gene annotations for the ncbigi database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_gene_product_annotation_wrong_ids[ncbigene] _______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:375: in test_gene_product_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no gene annotations for the ncbigene database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_gene_product_annotation_wrong_ids[ccds] _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:375: in test_gene_product_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no gene annotations for the ccds database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_gene_product_annotation_wrong_ids[hprd] _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:375: in test_gene_product_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no gene annotations for the hprd database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_gene_product_annotation_wrong_ids[asap] _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_annotation.py\u001b[0m:375: in test_gene_product_annotation_wrong_ids\n",
      "\u001b[1m    assert len(total) > 0, ann[\"message\"][db]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are no gene annotations for the asap database.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 > 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[31m\u001b[1m___________________ test_gene_protein_reaction_rule_presence ___________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:206: in test_gene_protein_reaction_rule_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are a total of 305 reactions (23.16%) without GPR:         ATPM,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     NMNP, SBTPD, PAPA160pp, PPND, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 305 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 305 = len(['ATPM', 'NMNP', 'SBTPD', 'PAPA160pp', 'PPND', 'Ktex', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________________ test_transport_reaction_gpr_presence _____________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:499: in test_transport_reaction_gpr_presence\n",
      "\u001b[1m    assert ann[\"metric\"] < 0.2, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are a total of 106 transport reactions (31.27% of all\u001b[0m\n",
      "\u001b[1m\u001b[31mE     transport reactions) without GPR:         MALTHXtexi, 12DGR120tipp,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     4PEPTtex, DDCAt2pp, MNtex, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0.31268436578171094 < 0.2\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________________ test_find_unique_metabolites _________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:555: in test_find_unique_metabolites\n",
      "\u001b[1m    assert len(ann[\"data\"]) < len(model.metabolites), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: Not counting the same entities in other compartments, there is a\u001b[0m\n",
      "\u001b[1m\u001b[31mE     total of 968 (100.00%) unique metabolites in the model:\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ala_L_asp__L_e, fa3_c, lald__L_c, mg2_c, murein3p3p_p, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 968 < 968\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 968 = len(['ala_L_asp__L_e', 'fa3_c', 'lald__L_c', 'mg2_c', 'murein3p3p_p', 'gly_pro__L_e', ...])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   968 = len([<Metabolite 10fthf_c at 0x7fd9ca261700>, <Metabolite 12dag3p_BS_c at 0x7fd9ca261f70>, <Metabolite 12dgr120_c at 0x7fd...abolite tyrglu_c at 0x7fd9ca9e8ac0>, <Metabolite tyrthr_c at 0x7fd9ca9e8b20>, <Metabolite gly_tyr_c at 0x7fd9ca9e8b80>])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +    where [<Metabolite 10fthf_c at 0x7fd9ca261700>, <Metabolite 12dag3p_BS_c at 0x7fd9ca261f70>, <Metabolite 12dgr120_c at 0x7fd...abolite tyrglu_c at 0x7fd9ca9e8ac0>, <Metabolite tyrthr_c at 0x7fd9ca9e8b20>, <Metabolite gly_tyr_c at 0x7fd9ca9e8b80>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7fd9ca2cde50>.metabolites\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_find_duplicate_metabolites_in_compartments ________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:584: in test_find_duplicate_metabolites_in_compartments\n",
      "\u001b[1m    len(ann[\"data\"]), truncate(ann[\"data\"])))\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/utils.py\u001b[0m:170: in truncate\n",
      "\u001b[1m    return \", \".join(sequence)\u001b[0m\n",
      "\u001b[1m\u001b[31mE   TypeError: sequence item 0: expected str instance, tuple found\u001b[0m\n",
      "\u001b[31m\u001b[1m___________ test_find_reactions_with_partially_identical_annotations ___________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:624: in test_find_reactions_with_partially_identical_annotations\n",
      "\u001b[1m    assert total == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: Based on annotations there are 139 different groups of overlapping\u001b[0m\n",
      "\u001b[1m\u001b[31mE     annotation which corresponds to a total of 317 duplicated reactions in\u001b[0m\n",
      "\u001b[1m\u001b[31mE     the model.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 317 == 0\u001b[0m\n",
      "\u001b[31m\u001b[1m________________________ test_find_duplicate_reactions _________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:660: in test_find_duplicate_reactions\n",
      "\u001b[1m    {}\"\"\".format(num, truncate(duplicates)))\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/utils.py\u001b[0m:168: in truncate\n",
      "\u001b[1m    return \", \".join(sequence[:LIST_SLICE] + [\"...\"])\u001b[0m\n",
      "\u001b[1m\u001b[31mE   TypeError: sequence item 0: expected str instance, tuple found\u001b[0m\n",
      "\u001b[31m\u001b[1m___________________ test_find_reactions_with_identical_genes ___________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:692: in test_find_reactions_with_identical_genes\n",
      "\u001b[1m    assert num_dup == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: Based only on equal genes there are 154 different groups of\u001b[0m\n",
      "\u001b[1m\u001b[31mE     identical reactions which corresponds to a total of 601\u001b[0m\n",
      "\u001b[1m\u001b[31mE     duplicated reactions in the model.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 601 == 0\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________________ test_find_medium_metabolites _________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_basic.py\u001b[0m:713: in test_find_medium_metabolites\n",
      "\u001b[1m    ann[\"metric\"] = len(ann[\"data\"]) / num_ex\u001b[0m\n",
      "\u001b[1m\u001b[31mE   TypeError: unsupported operand type(s) for /: 'int' and 'list'\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________________ test_biomass_consistency[Growth] _______________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py\u001b[0m:121: in test_biomass_consistency\n",
      "\u001b[1m    assert outcome, ann[\"message\"][reaction_id]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: The component molar mass of the biomass reaction Growth sums up to\u001b[0m\n",
      "\u001b[1m\u001b[31mE     1.0300277967729958             which is outside of the 1e-03 margin\u001b[0m\n",
      "\u001b[1m\u001b[31mE     from 1 mmol / g[CDW] / h.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert False\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________________ test_fast_growth_default[Growth] _______________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py\u001b[0m:370: in test_fast_growth_default\n",
      "\u001b[1m    assert outcome, ann[\"message\"][reaction_id]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: Using the biomass reaction Growth and when the model is simulated on\u001b[0m\n",
      "\u001b[1m\u001b[31mE     the provided default medium the growth rate is *lower* than that\u001b[0m\n",
      "\u001b[1m\u001b[31mE     of the fastest bacteria. This is to be expected for             a\u001b[0m\n",
      "\u001b[1m\u001b[31mE     majority of organisms.\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert False\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________ test_essential_precursors_not_in_biomass[Growth] _______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_biomass.py\u001b[0m:494: in test_essential_precursors_not_in_biomass\n",
      "\u001b[1m    assert len(ann[\"data\"][reaction_id]) == 0, ann[\"message\"][reaction_id]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: Growth lacks a total of 1 essential metabolites         (1.72% of all\u001b[0m\n",
      "\u001b[1m\u001b[31mE     biomass precursors). Specifically         these are: ['fmn_c'].\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 1 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 1 = len(['fmn_c'])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________________ test_reaction_charge_balance _________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:158: in test_reaction_charge_balance\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 3 (0.26%) reactions are charge unbalanced with at\u001b[0m\n",
      "\u001b[1m\u001b[31mE     least one of the metabolites not having a charge or the overall\u001b[0m\n",
      "\u001b[1m\u001b[31mE     charge not equal to 0: BTS2, G3POA_BS, AGPATr_BS\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 3 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 3 = len(['BTS2', 'G3POA_BS', 'AGPATr_BS'])\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________________ test_reaction_mass_balance __________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:193: in test_reaction_mass_balance\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 2 (0.17%) reactions are mass unbalanced with at least\u001b[0m\n",
      "\u001b[1m\u001b[31mE     one of the metabolites not having a formula or the overall mass not\u001b[0m\n",
      "\u001b[1m\u001b[31mE     equal to 0: G3POA_BS, AGPATr_BS\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 2 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 2 = len(['G3POA_BS', 'AGPATr_BS'])\u001b[0m\n",
      "\u001b[31m\u001b[1m____________________________ test_blocked_reactions ____________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:222: in test_blocked_reactions\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are 98 (7.44%) blocked reactions in         the model: EX_btn_e,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     EX_chol_e, EX_rmn_e, EX_spmd_e, EX_xyl__D_e, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 98 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 98 = len(['EX_btn_e', 'EX_chol_e', 'EX_rmn_e', 'EX_spmd_e', 'EX_xyl__D_e', 'ALDD22x', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________ test_find_stoichiometrically_balanced_cycles _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:246: in test_find_stoichiometrically_balanced_cycles\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: There are 111 (8.43%) reactions         which participate in SBC in\u001b[0m\n",
      "\u001b[1m\u001b[31mE     the model: 13PPDH, 13PPDH2, 4ABUTD, ABUTD, ACCOAL, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 111 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 111 = len(['13PPDH', '13PPDH2', '4ABUTD', 'ABUTD', 'ACCOAL', 'ACKr', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m______________________________ test_find_orphans _______________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:271: in test_find_orphans\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 42 (4.34%) metabolites are not produced by any reaction\u001b[0m\n",
      "\u001b[1m\u001b[31mE     of the model: cl_p, inost_c, aproa_c, id3acald_c, im4act_c, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 42 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 42 = len(['cl_p', 'inost_c', 'aproa_c', 'id3acald_c', 'im4act_c', 'imzacd_c', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m______________________________ test_find_deadends ______________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:295: in test_find_deadends\n",
      "\u001b[1m    assert ann[\"data\"] == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 45 (4.65%) metabolites are not consumed by any reaction\u001b[0m\n",
      "\u001b[1m\u001b[31mE     of the model: 2ins_c, spmd_c, ind3ac_c, im4ac_c, imzac_c, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert ['2ins_c', 'spmd_c', 'ind3ac_c', 'im4ac_c', 'imzac_c', '4aabutn_c', ...] == 0\u001b[0m\n",
      "\u001b[31m\u001b[1m____________________________ test_find_disconnected ____________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:319: in test_find_disconnected\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 5 (0.52%) metabolites are not associated with any\u001b[0m\n",
      "\u001b[1m\u001b[31mE     reaction of the model: 3php_c, pa160140_c, pa160180_c, pa160205n3_c,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     pa160226n3_c\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 5 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 5 = len(['3php_c', 'pa160140_c', 'pa160180_c', 'pa160205n3_c', 'pa160226n3_c'])\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________ test_find_metabolites_not_produced_with_open_bounds ______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:349: in test_find_metabolites_not_produced_with_open_bounds\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 250 (25.83%) metabolites cannot be produced in complete\u001b[0m\n",
      "\u001b[1m\u001b[31mE     medium: 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr161_c,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 250 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 250 = len(['12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr161_c', '12dgr161_p', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________ test_find_metabolites_not_consumed_with_open_bounds ______________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:379: in test_find_metabolites_not_consumed_with_open_bounds\n",
      "\u001b[1m    assert len(ann[\"data\"]) == 0, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 255 (26.34%) metabolites cannot be consumed in complete\u001b[0m\n",
      "\u001b[1m\u001b[31mE     medium: 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr161_c,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 255 == 0\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 255 = len(['12dgr120_c', '12dgr120_p', '12dgr140_c', '12dgr140_p', '12dgr161_c', '12dgr161_p', ...])\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________ test_find_reactions_unbounded_flux_default_condition _____________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_consistency.py\u001b[0m:413: in test_find_reactions_unbounded_flux_default_condition\n",
      "\u001b[1m    assert ann[\"metric\"] <= 0.1, ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError:  A fraction of 22.32% of the non-blocked reactions (in total 98\u001b[0m\n",
      "\u001b[1m\u001b[31mE     reactions) can carry unbounded flux in the default model\u001b[0m\n",
      "\u001b[1m\u001b[31mE     condition. Unbounded reactions may be involved in\u001b[0m\n",
      "\u001b[1m\u001b[31mE     thermodynamically infeasible cycles: 13PPDH, 13PPDH2, 4ABUTD, ABUTD,\u001b[0m\n",
      "\u001b[1m\u001b[31mE     ACCOAL, ...\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0.22323462414578588 <= 0.1\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________________________ test_sbml_level ________________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py\u001b[0m:39: in test_sbml_level\n",
      "\u001b[1m    sbml_version[0], sbml_version[1])\u001b[0m\n",
      "\u001b[1m\u001b[31mE   TypeError: 'NoneType' object is not subscriptable\u001b[0m\n",
      "\u001b[31m\u001b[1m______________________________ test_fbc_presence _______________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbml.py\u001b[0m:66: in test_fbc_presence\n",
      "\u001b[1m    fbc_present = sbml_version[2] is not None\u001b[0m\n",
      "\u001b[1m\u001b[31mE   TypeError: 'NoneType' object is not subscriptable\u001b[0m\n",
      "\u001b[31m\u001b[1m_________________________ test_metabolite_sbo_presence _________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:58: in test_metabolite_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(model.metabolites), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 metabolites (0.00%) lack annotation with any type\u001b[0m\n",
      "\u001b[1m\u001b[31mE     of SBO term:\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 968\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   968 = len([<Metabolite 10fthf_c at 0x7fd9ca261700>, <Metabolite 12dag3p_BS_c at 0x7fd9ca261f70>, <Metabolite 12dgr120_c at 0x7fd...abolite tyrglu_c at 0x7fd9ca9e8ac0>, <Metabolite tyrthr_c at 0x7fd9ca9e8b20>, <Metabolite gly_tyr_c at 0x7fd9ca9e8b80>])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +    where [<Metabolite 10fthf_c at 0x7fd9ca261700>, <Metabolite 12dag3p_BS_c at 0x7fd9ca261f70>, <Metabolite 12dgr120_c at 0x7fd...abolite tyrglu_c at 0x7fd9ca9e8ac0>, <Metabolite tyrthr_c at 0x7fd9ca9e8b20>, <Metabolite gly_tyr_c at 0x7fd9ca9e8b80>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7fd9ca2cde50>.metabolites\u001b[0m\n",
      "\u001b[31m\u001b[1m__________________________ test_reaction_sbo_presence __________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:88: in test_reaction_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(model.reactions), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 reactions (0.00%) lack annotation with any type\u001b[0m\n",
      "\u001b[1m\u001b[31mE     of SBO term:\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 1317\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   1317 = len([<Reaction 12DGR120tipp at 0x7fd9caa08580>, <Reaction 12DGR140tipp at 0x7fd9c7cc18b0>, <Reaction 12DGR160tipp at 0x7fd...fd9c7bf8eb0>, <Reaction KAS8 at 0x7fd9cac6feb0>, <Reaction NNDPR at 0x7fd9cac6fcd0>, <Reaction PPND at 0x7fd9cac6fa90>])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +    where [<Reaction 12DGR120tipp at 0x7fd9caa08580>, <Reaction 12DGR140tipp at 0x7fd9c7cc18b0>, <Reaction 12DGR160tipp at 0x7fd...fd9c7bf8eb0>, <Reaction KAS8 at 0x7fd9cac6feb0>, <Reaction NNDPR at 0x7fd9cac6fcd0>, <Reaction PPND at 0x7fd9cac6fa90>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7fd9ca2cde50>.reactions\u001b[0m\n",
      "\u001b[31m\u001b[1m____________________________ test_gene_sbo_presence ____________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:117: in test_gene_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(model.genes), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 genes (0.00%) lack annotation with any type of\u001b[0m\n",
      "\u001b[1m\u001b[31mE     SBO term:\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 601\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   601 = len([<Gene WP_012290939_1 at 0x7fd9caa08550>, <Gene WP_012290272_1 at 0x7fd9caa085e0>, <Gene WP_002842355_1 at 0x7fd9caa08...7fd9c7cc11c0>, <Gene FMG_0827 at 0x7fd9c7cc1190>, <Gene FMG_1032 at 0x7fd9c7cc1130>, <Gene FMG_0500 at 0x7fd9c7cc10d0>])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +    where [<Gene WP_012290939_1 at 0x7fd9caa08550>, <Gene WP_012290272_1 at 0x7fd9caa085e0>, <Gene WP_002842355_1 at 0x7fd9caa08...7fd9c7cc11c0>, <Gene FMG_0827 at 0x7fd9c7cc1190>, <Gene FMG_1032 at 0x7fd9c7cc1130>, <Gene FMG_0500 at 0x7fd9c7cc10d0>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7fd9ca2cde50>.genes\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_metabolic_reaction_specific_sbo_presence _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:150: in test_metabolic_reaction_specific_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(pure), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 metabolic reactions (0.00% of all purely\u001b[0m\n",
      "\u001b[1m\u001b[31mE     metabolic reactions) lack annotation with the SBO term\u001b[0m\n",
      "\u001b[1m\u001b[31mE     \"SBO:0000176\" for 'biochemical reaction':\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 818\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   818 = len({<Reaction MDDEP4pp at 0x7fd9c7d180d0>, <Reaction MCTP2App at 0x7fd9c7d18340>, <Reaction ACGAMPM at 0x7fd9c7ce8370>, <Reaction 2AGPEAT180 at 0x7fd9c7cf4eb0>, <Reaction TDPDRR at 0x7fd9c7fa0400>, <Reaction NTPP10 at 0x7fd9c7ef4ee0>, ...})\u001b[0m\n",
      "\u001b[31m\u001b[1m________________ test_transport_reaction_specific_sbo_presence _________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:188: in test_transport_reaction_specific_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(transports), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 metabolic reactions (0.00% of all transport\u001b[0m\n",
      "\u001b[1m\u001b[31mE     reactions) lack annotation with one of the SBO terms: ['SBO:0000185',\u001b[0m\n",
      "\u001b[1m\u001b[31mE     'SBO:0000588', 'SBO:0000587', 'SBO:0000655', 'SBO:0000654',\u001b[0m\n",
      "\u001b[1m\u001b[31mE     'SBO:0000660', 'SBO:0000659', 'SBO:0000657', 'SBO:0000658'] for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     'biochemical reaction':\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 339\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   339 = len({<Reaction GLCptspp at 0x7fd9c80e8070>, <Reaction MALTabc at 0x7fd9c7d10370>, <Reaction TYRabc at 0x7fd9c7b203d0>, <Re...n MALTHXtexi at 0x7fd9c7d104f0>, <Reaction 12DGR120tipp at 0x7fd9caa08580>, <Reaction ACTNabc1 at 0x7fd9c7d185b0>, ...})\u001b[0m\n",
      "\u001b[31m\u001b[1m____________________ test_metabolite_specific_sbo_presence _____________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:218: in test_metabolite_specific_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(model.metabolites), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 transport reactions (0.00% of all metabolites)\u001b[0m\n",
      "\u001b[1m\u001b[31mE     lack annotation with the SBO term \"SBO:0000247\" for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     'simple chemical':\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 968\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   968 = len([<Metabolite 10fthf_c at 0x7fd9ca261700>, <Metabolite 12dag3p_BS_c at 0x7fd9ca261f70>, <Metabolite 12dgr120_c at 0x7fd...abolite tyrglu_c at 0x7fd9ca9e8ac0>, <Metabolite tyrthr_c at 0x7fd9ca9e8b20>, <Metabolite gly_tyr_c at 0x7fd9ca9e8b80>])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +    where [<Metabolite 10fthf_c at 0x7fd9ca261700>, <Metabolite 12dag3p_BS_c at 0x7fd9ca261f70>, <Metabolite 12dgr120_c at 0x7fd...abolite tyrglu_c at 0x7fd9ca9e8ac0>, <Metabolite tyrthr_c at 0x7fd9ca9e8b20>, <Metabolite gly_tyr_c at 0x7fd9ca9e8b80>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7fd9ca2cde50>.metabolites\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________________ test_gene_specific_sbo_presence ________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:248: in test_gene_specific_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(model.genes), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 genes (0.00% of all genes) lack             annotation\u001b[0m\n",
      "\u001b[1m\u001b[31mE     with the SBO term \"SBO:0000243\" for             'gene':\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 601\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   601 = len([<Gene WP_012290939_1 at 0x7fd9caa08550>, <Gene WP_012290272_1 at 0x7fd9caa085e0>, <Gene WP_002842355_1 at 0x7fd9caa08...7fd9c7cc11c0>, <Gene FMG_0827 at 0x7fd9c7cc1190>, <Gene FMG_1032 at 0x7fd9c7cc1130>, <Gene FMG_0500 at 0x7fd9c7cc10d0>])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +    where [<Gene WP_012290939_1 at 0x7fd9caa08550>, <Gene WP_012290272_1 at 0x7fd9caa085e0>, <Gene WP_002842355_1 at 0x7fd9caa08...7fd9c7cc11c0>, <Gene FMG_0827 at 0x7fd9c7cc1190>, <Gene FMG_1032 at 0x7fd9c7cc1130>, <Gene FMG_0500 at 0x7fd9c7cc10d0>] = <Model finegoldia_magna_ATCC_29328_2_2_raw at 0x7fd9ca2cde50>.genes\u001b[0m\n",
      "\u001b[31m\u001b[1m_____________________ test_exchange_specific_sbo_presence ______________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:290: in test_exchange_specific_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(exchanges), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 exchange reactions (0.00% of all exchange\u001b[0m\n",
      "\u001b[1m\u001b[31mE     reactions) lack annotation with the SBO term \"SBO:0000627\" for\u001b[0m\n",
      "\u001b[1m\u001b[31mE     'exchange reaction':\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 157\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   157 = len([<Reaction EX_14glucan_e at 0x7fd9c8391940>, <Reaction EX_15dap_e at 0x7fd9c8391370>, <Reaction EX_26dap__M_e at 0x7fd...Reaction EX_atp_e at 0x7fd9c7ab9e50>, <Reaction EX_pan4p_e at 0x7fd9c7ab9e80>, <Reaction EX_dpcoa_e at 0x7fd9c7ab9c10>])\u001b[0m\n",
      "\u001b[31m\u001b[1m_______________________ test_sink_specific_sbo_presence ________________________\u001b[0m\n",
      "\u001b[1m\u001b[31m/home/salatan/anaconda3/lib/python3.8/site-packages/memote/suite/tests/test_sbo.py\u001b[0m:376: in test_sink_specific_sbo_presence\n",
      "\u001b[1m    assert len(ann[\"data\"]) == len(sinks), ann[\"message\"]\u001b[0m\n",
      "\u001b[1m\u001b[31mE   AssertionError: A total of 0 genes (0.00% of all sink reactions) lack\u001b[0m\n",
      "\u001b[1m\u001b[31mE     annotation with the SBO term \"SBO:0000632\" for         'sink\u001b[0m\n",
      "\u001b[1m\u001b[31mE     reaction':\u001b[0m\n",
      "\u001b[1m\u001b[31mE   assert 0 == 2\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  where 0 = len([])\u001b[0m\n",
      "\u001b[1m\u001b[31mE    +  and   2 = len([<Reaction sink_lipopb_c at 0x7fd9c8391d90>, <Reaction sink_mobd_c at 0x7fd9c804cd90>])\u001b[0m\n",
      "\u001b[33m=============================== warnings summary ===============================\u001b[0m\n",
      "/home/salatan/anaconda3/lib/python3.8/site-packages/memote/support/thermodynamics.py:23\n",
      "  /home/salatan/anaconda3/lib/python3.8/site-packages/memote/support/thermodynamics.py:23: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3, and in 3.9 it will stop working\n",
      "    from collections import Iterable, defaultdict\n",
      "\n",
      "-- Docs: https://docs.pytest.org/en/latest/warnings.html\n",
      "\u001b[31m\u001b[1m======== 77 failed, 49 passed, 19 skipped, 1 warnings in 22.92 seconds =========\u001b[0m\n"
     ]
    }
   ],
   "source": [
    "!python annotate_reactions.py \"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.mp2.xml\" \"2.2/finegoldia_magna_ATCC_29328_2.2.fo.ch.mp.mcb.lt.re.ar.gpr.pw.gf1.gfmm.gf2.gfco3.circ.mcb2.sbo.eco.mp2.re.xml\" \"2.2/tables/reactions_not_in_bigg_2.tsv\" \"2.2/memote-reports/annotated_genes_2.html\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "7edbfe03-6bf9-464c-acf0-f9498dbf1a71",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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