From e12750b3a19b2024e74aa49a5dbdc3fce7a9c448 Mon Sep 17 00:00:00 2001 From: Simon Rogers Date: Mon, 29 Oct 2018 21:00:02 +0000 Subject: [PATCH] added pipfile.lock (as recommended here https://github.com/pypa/pipenv/issues/598) and removed a couple of things from requirements.txt and pipfile to make it compatible with linux --- Pipfile | 2 - Pipfile.lock | 648 +++++++++++++++++++++ prototype/nplinker_example_script.py.ipynb | 194 +++--- requirements.txt | 2 - 4 files changed, 742 insertions(+), 104 deletions(-) create mode 100644 Pipfile.lock diff --git a/Pipfile b/Pipfile index 2979a132..d77f22aa 100644 --- a/Pipfile +++ b/Pipfile @@ -14,8 +14,6 @@ decorator = "==4.3.0" defusedxml = "==0.5.0" entrypoints = "==0.2.3" "enum34" = "==1.1.6" -"functools32" = "==3.2.3.post2" -futures = "==3.2.0" ipaddress = "==1.0.22" ipykernel = "==4.10.0" ipython = "==5.8.0" diff --git a/Pipfile.lock b/Pipfile.lock new file mode 100644 index 00000000..3547ea3a --- /dev/null +++ b/Pipfile.lock @@ -0,0 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--- a/prototype/nplinker_example_script.py.ipynb +++ b/prototype/nplinker_example_script.py.ipynb @@ -21,30 +21,24 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "from nplinker_constants import nplinker_setup\n", - "nplinker_setup(LDA_PATH='/Users/simon/git/lda/code')" + "nplinker_setup(LDA_PATH='/home/simon/git/lda/code')" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 5, "metadata": {}, "outputs": [ { - "ename": "FileNotFoundError", - "evalue": "[Errno 2] No such file or directory: '/srv/data/crusemann/gnps/METABOLOMICS-SNETS-c36f90ba-download_clustered_spectra-main.mgf'", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mFileNotFoundError\u001b[0m Traceback (most recent call last)", - "\u001b[0;32m\u001b[0m in \u001b[0;36m\u001b[0;34m\u001b[0m\n\u001b[1;32m 1\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mmetabolomics\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mload_spectra\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 2\u001b[0m \u001b[0mmgf_file\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'/srv/data/crusemann/gnps/METABOLOMICS-SNETS-c36f90ba-download_clustered_spectra-main.mgf'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mspectra\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mload_spectra\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmgf_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m", - "\u001b[0;32m~/git/nplinker/prototype/metabolomics.py\u001b[0m in \u001b[0;36mload_spectra\u001b[0;34m(mgf_file)\u001b[0m\n\u001b[1;32m 116\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mload_spectra\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmgf_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 117\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mms2lda_feature_extraction\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mLoadMGF\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 118\u001b[0;31m \u001b[0mms1\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mms2\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mmetadata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mLoadMGF\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mname_field\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'scans'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mload_spectra\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mmgf_file\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 119\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\"Loaded {} molecules\"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mformat\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mms1\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 120\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mmols_to_spectra\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mms2\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0mmetadata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;32m~/git/lda/code/ms2lda_feature_extraction.py\u001b[0m in \u001b[0;36mload_spectra\u001b[0;34m(self, input_set)\u001b[0m\n\u001b[1;32m 1386\u001b[0m \u001b[0;31m## Use built-in method to get file_name\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1387\u001b[0m \u001b[0mfile_name\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mos\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mpath\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbasename\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput_file\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1388\u001b[0;31m \u001b[0;32mwith\u001b[0m \u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0minput_file\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m'r'\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0mf\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1389\u001b[0m \u001b[0mtemp_metadata\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1390\u001b[0m \u001b[0min_doc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", - "\u001b[0;31mFileNotFoundError\u001b[0m: [Errno 2] No such file or directory: '/srv/data/crusemann/gnps/METABOLOMICS-SNETS-c36f90ba-download_clustered_spectra-main.mgf'" + "name": "stdout", + "output_type": "stream", + "text": [ + "Loaded 5930 molecules\n" ] } ], @@ -56,7 +50,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -65,7 +59,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -75,17 +69,91 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 9, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ + "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", + "[('Massbank:FFF00078 Stigmastanol', 'gnps')]\n", + "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", + "[('Massbank:FFF00098 24-Ethylcoprostanol', 'gnps')]\n", + "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", + "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", + "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", + "[('(2R,3R,4S,6R)-2-((10-hydroxy-2,2-dimethyl-3,4-dihydro-2H-benzo[g]chromen-5-yl)oxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol', 'gnps')]\n", + "[('MLS001060855-01!', 'gnps')]\n", + "[('Massbank:CE000164 S,R-Noscapine', 'gnps')]\n", + "[('MLS000876958-01!2-(3,4-dimethoxyphenyl)-5-hydroxy-3,6,7,8-tetramethoxychromen-4-one', 'gnps')]\n", + "[('Sevadicin', 'gnps')]\n", + "[('MLS000830274-01!Ethmozine', 'gnps')]\n", + "[('8-desoxyenterocin', 'gnps')]\n", + "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", + "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", + "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", + "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", + "[('ReSpect:PS087410 Vitexin|Vitx|apigenin-8-C-glucoside|8-beta-D-Glucopyranosyl-apigenin|Orientoside', 'gnps')]\n", + "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", + "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", + "[('B21A03', 'gnps')]\n", + "[('Enterocin', 'gnps')]\n", + "[('HMDB:HMDB00631-862 Deoxycholic acid glycine conjugate', 'gnps')]\n", + "[('Massbank:BML00870 11-(2-bromo-3,6-dimethoxyphenyl)-3,3-dimethyl-2,3,4-trihydro-5H,10H,11H-benzo[ b]benzo[2,1-f]1,4-diazepin-1-one', 'gnps')]\n", + "[('Glycocholic acid', 'gnps')]\n", + "[('Glycocholic acid', 'gnps')]\n", + "[('Staurosporine', 'gnps')]\n", + "[('Staurosporine', 'gnps')]\n", + "[('Loperamide hydrochloride', 'gnps')]\n", + "[('Massbank:PR040097 Isorhamnetin-3-O-glucoside|Isor_3_Glc|5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-4-one', 'gnps')]\n", + "[('7-OH-staurosporine', 'gnps')]\n", + "[('7-OH-staurosporine', 'gnps')]\n", + "[('7-OH-staurosporine', 'gnps')]\n", + "[('7-OH-staurosporine', 'gnps')]\n", + "[('7-OH-staurosporine', 'gnps')]\n", + "[(\"CYTIDINE 5'-DIPHOSPHOCHOLINE\", 'gnps')]\n", + "[('1-Palmitoyl-sn-glycero-3-phosphocholine', 'gnps')]\n", + "[('Alteramide B', 'gnps')]\n", + "[('MLS000563039-01!', 'gnps')]\n", + "[('1-Oleoyl-sn-glycero-3-phosphocholine', 'gnps')]\n", + "[('Antimycin A1', 'gnps')]\n", + "[('Massbank:EA285507 Dronedarone|N-[2-butyl-3-[4-[3-(dibutylamino)propoxy]benzoyl]-1-benzofuran-5-yl]methanesulfonamide', 'gnps')]\n", + "[('MLS000028713-01!DEFEROXAMINE MESYLATE', 'gnps')]\n", + "[('Rosamicin', 'gnps')]\n", + "[('Rosamicin', 'gnps')]\n", + "[('MLS000863563-01!1,11,22-trihydroxy-1,6,11,16,22,27-hexazacyclodotriacontane-2,5,12,15,23,26-hexone', 'gnps')]\n", + "[('MLS000863563-01!1,11,22-trihydroxy-1,6,11,16,22,27-hexazacyclodotriacontane-2,5,12,15,23,26-hexone', 'gnps')]\n", + "[('21-hydroxyrosamicin ', 'gnps')]\n", + "[('21-hydroxyrosamicin ', 'gnps')]\n", + "[('21-hydroxyrosamicin ', 'gnps')]\n", + "[('18-dihydro-21-hydroxyrosamicin ', 'gnps')]\n", + "[('Desferrioxamine E', 'gnps')]\n", + "[('Desferrioxamine E', 'gnps')]\n", + "[('Desferrioxamine E', 'gnps')]\n", + "[(\"ReSpect:PT212210 Cyanidin-3-O-(2''-O-beta-glucopyranosyl-beta-glucopyranoside)|Cy 3-Soph|cyanidin-3-sophoroside|(2S,3R,4S,5S,6R)-2-[(2S,3R,4S,5S,6R)-2-[2-(3,4-dihydroxyphenyl)-5,7-dihydroxychromenylium-3-yl]oxy-4,5-di\", 'gnps')]\n", + "[('Desferrioxamine E', 'gnps')]\n", + "[('GranisetronHCl', 'gnps')]\n", + "[('GranisetronHCl', 'gnps')]\n", + "[('Progesterone', 'gnps')]\n", + "[('Rifamycin W', 'gnps')]\n", + "[('Rifamycin W', 'gnps')]\n", + "[('Arenimycin A', 'gnps')]\n", + "[('Arenimycin A', 'gnps')]\n", + "[('Lomaiviticin C', 'gnps')]\n", + "[('Lomaiviticin D', 'gnps')]\n", "[('Lomaiviticin A', 'gnps')]\n", + "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", + "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", + "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", + "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", + "[('Rifamycin S', 'gnps')]\n", + "[('Acyl desferrioxamine C13', 'gnps')]\n", + "[('Acyl desferrioxamine C15', 'gnps')]\n", + "[('Arenimycin B', 'gnps')]\n", + "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", - "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", @@ -102,108 +170,34 @@ "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", - "[('Staurosporine', 'gnps')]\n", - "[('Staurosporine', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('desmethylsalinamide E', 'gnps')]\n", "[('Salinamide E', 'gnps')]\n", - "[('Rosamicin', 'gnps')]\n", - "[('Enterocin', 'gnps')]\n", - "[('HMDB:HMDB00631-862 Deoxycholic acid glycine conjugate', 'gnps')]\n", - "[('Sodium Formate', 'gnps')]\n", - "[('GranisetronHCl', 'gnps')]\n", - "[('GranisetronHCl', 'gnps')]\n", - "[('Progesterone', 'gnps')]\n", - "[('Massbank:BML00870 11-(2-bromo-3,6-dimethoxyphenyl)-3,3-dimethyl-2,3,4-trihydro-5H,10H,11H-benzo[ b]benzo[2,1-f]1,4-diazepin-1-one', 'gnps')]\n", - "[('7-OH-staurosporine', 'gnps')]\n", - "[('MLS000863563-01!1,11,22-trihydroxy-1,6,11,16,22,27-hexazacyclodotriacontane-2,5,12,15,23,26-hexone', 'gnps')]\n", - "[('MLS000863563-01!1,11,22-trihydroxy-1,6,11,16,22,27-hexazacyclodotriacontane-2,5,12,15,23,26-hexone', 'gnps')]\n", - "[('Desferrioxamine E', 'gnps')]\n", - "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", "[('Ammosamide B trimer', 'gnps')]\n", - "[('21-hydroxyrosamicin ', 'gnps')]\n", - "[('MLS000830274-01!Ethmozine', 'gnps')]\n", - "[('21-hydroxyrosamicin ', 'gnps')]\n", - "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", - "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", - "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", - "[('ReSpect:PS087410 Vitexin|Vitx|apigenin-8-C-glucoside|8-beta-D-Glucopyranosyl-apigenin|Orientoside', 'gnps')]\n", - "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", - "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", - "[('MLS000876958-01!2-(3,4-dimethoxyphenyl)-5-hydroxy-3,6,7,8-tetramethoxychromen-4-one', 'gnps')]\n", + "[('Sodium Formate', 'gnps')]\n", + "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('Salinamide A', 'gnps')]\n", "[('Cyclomarin A', 'gnps')]\n", - "[('Massbank:EA285507 Dronedarone|N-[2-butyl-3-[4-[3-(dibutylamino)propoxy]benzoyl]-1-benzofuran-5-yl]methanesulfonamide', 'gnps')]\n", - "[('MLS000028713-01!DEFEROXAMINE MESYLATE', 'gnps')]\n", - "[('1-Palmitoyl-sn-glycero-3-phosphocholine', 'gnps')]\n", - "[('Alteramide B', 'gnps')]\n", "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", - "[('B21A03', 'gnps')]\n", - "[('(2R,3R,4S,6R)-2-((10-hydroxy-2,2-dimethyl-3,4-dihydro-2H-benzo[g]chromen-5-yl)oxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol', 'gnps')]\n", - "[('Loperamide hydrochloride', 'gnps')]\n", + "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", "[('Salinamide B', 'gnps')]\n", - "[('21-hydroxyrosamicin ', 'gnps')]\n", - "[('18-dihydro-21-hydroxyrosamicin ', 'gnps')]\n", - "[('Desferrioxamine E', 'gnps')]\n", - "[('Desferrioxamine E', 'gnps')]\n", - "[('Desferrioxamine E', 'gnps')]\n", "[('pumilacidin_E_14342_dereplictor_pv_1.13518e-25', 'gnps')]\n", - "[('Antimycin A1', 'gnps')]\n", - "[('MLS000563039-01!', 'gnps')]\n", - "[('Arenimycin A', 'gnps')]\n", - "[('Arenimycin A', 'gnps')]\n", - "[('Lomaiviticin C', 'gnps')]\n", - "[('Rifamycin W', 'gnps')]\n", - "[('Rifamycin W', 'gnps')]\n", - "[(\"CYTIDINE 5'-DIPHOSPHOCHOLINE\", 'gnps')]\n", - "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", - "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", - "[('1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine', 'gnps')]\n", - "[('Rifamycin S', 'gnps')]\n", - "[('Lomaiviticin D', 'gnps')]\n", - "[('Rosamicin', 'gnps')]\n", - "[('Acyl desferrioxamine C15', 'gnps')]\n", - "[('Glycocholic acid', 'gnps')]\n", - "[('Glycocholic acid', 'gnps')]\n", - "[('MLS001060855-01!', 'gnps')]\n", - "[('Massbank:CE000164 S,R-Noscapine', 'gnps')]\n", - "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", - "[('Massbank:FFF00078 Stigmastanol', 'gnps')]\n", - "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", - "[('Massbank:FFF00098 24-Ethylcoprostanol', 'gnps')]\n", - "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", - "[('Sorbitane Monopalmitate - Polysorbate 40 in-source fragment', 'gnps')]\n", "[('Aurantin_II_24051_dereplictor_pv_9.12748e-26', 'gnps')]\n", - "[('Actinomycin_X2;_Actinomycin_V;_Actinomyc_28731_dereplictor_pv_1.70529e-21', 'gnps')]\n", - "[('1-Oleoyl-sn-glycero-3-phosphocholine', 'gnps')]\n", - "[('Massbank:PR040097 Isorhamnetin-3-O-glucoside|Isor_3_Glc|5,7-dihydroxy-2-(4-hydroxy-3-methoxyphenyl)-3-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxychromen-4-one', 'gnps')]\n", - "[('7-OH-staurosporine', 'gnps')]\n", - "[('7-OH-staurosporine', 'gnps')]\n", - "[('7-OH-staurosporine', 'gnps')]\n", - "[('7-OH-staurosporine', 'gnps')]\n", - "[('Acyl desferrioxamine C13', 'gnps')]\n", - "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", - "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n", - "[('8-desoxyenterocin', 'gnps')]\n", - "[(\"ReSpect:PT212210 Cyanidin-3-O-(2''-O-beta-glucopyranosyl-beta-glucopyranoside)|Cy 3-Soph|cyanidin-3-sophoroside|(2S,3R,4S,5S,6R)-2-[(2S,3R,4S,5S,6R)-2-[2-(3,4-dihydroxyphenyl)-5,7-dihydroxychromenylium-3-yl]oxy-4,5-di\", 'gnps')]\n", - "[('Sevadicin', 'gnps')]\n", - "[('Arenimycin B', 'gnps')]\n", - "[('Sorbitane Monostearate - Polysorbate 60 in-source fragment', 'gnps')]\n", - "[('MS_Contaminant_Sodium_Formate_Cluster', 'gnps')]\n" + "[('Actinomycin_X2;_Actinomycin_V;_Actinomyc_28731_dereplictor_pv_1.70529e-21', 'gnps')]\n" ] } ], "source": [ "for s in spectra:\n", " if len(s.annotations) > 0:\n", - " print s.annotations\n", + " print(s.annotations)\n", "\n" ] }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 10, "metadata": {}, "outputs": [], "source": [ @@ -216,7 +210,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 11, "metadata": {}, "outputs": [], "source": [ @@ -251,7 +245,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 12, "metadata": {}, "outputs": [], "source": [ @@ -1847,7 +1841,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.0" + "version": "3.6.5" } }, "nbformat": 4, diff --git a/requirements.txt b/requirements.txt index 770fc54c..a25c53c9 100644 --- a/requirements.txt +++ b/requirements.txt @@ -10,8 +10,6 @@ decorator==4.3.0 defusedxml==0.5.0 entrypoints==0.2.3 enum34==1.1.6 -functools32==3.2.3.post2 -futures==3.2.0 ipaddress==1.0.22 ipykernel==4.10.0 ipython==5.8.0