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{ | ||
"cells": [ | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"# Reading a _Gene Product Association Data_ (GPAD) file" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"1. Download a GPAD file\n", | ||
"2. Load the GPAD file into the GpadReader\n", | ||
"3. Get Annotations\n", | ||
"\n", | ||
"**Bonus: Each line in the GPAD file is stored in a namedtuple**:\n", | ||
" * Namedtuple fields\n", | ||
" * Print a subset of the namedtuple fields" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## 1) Download a GPAD file and GO Dag file" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 1, | ||
"metadata": { | ||
"scrolled": true | ||
}, | ||
"outputs": [], | ||
"source": [ | ||
"from os.path import exists\n", | ||
"if not exists('goa_human.gpad'):\n", | ||
" !rm -f goa_human.gpad.gz\n", | ||
" !wget http://current.geneontology.org/annotations/goa_human.gpad.gz\n", | ||
" !gunzip goa_human.gpad.gz" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 2, | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"if not exists('go-basic.obo'):\n", | ||
" !wget http://geneontology.org/ontology/go-basic.obo" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## 2) Load the GPAD file into the GpadReader" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 3, | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
" EXISTS: go-basic.obo\n", | ||
"go-basic.obo: fmt(1.2) rel(2022-11-03) 46,800 Terms\n", | ||
"HMS:0:00:16.880690 635,765 annotations READ: goa_human.gpad \n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"from goatools.base import get_godag\n", | ||
"from goatools.anno.gpad_reader import GpadReader\n", | ||
"\n", | ||
"godag = get_godag(\"go-basic.obo\")\n", | ||
"anno = GpadReader(\"goa_human.gpad\", godag=godag)" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## 3) Get Annotations\n", | ||
"The annotations will be stored in three dicts, one for each GODAG branch, where:\n", | ||
" * the key is the protein ID and \n", | ||
" * the value is a list of GO IDs associated with the protein." | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 4, | ||
"metadata": {}, | ||
"outputs": [], | ||
"source": [ | ||
"ns2assc = anno.get_ns2assc()" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 5, | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"MF A0A024RBG1 : GO:0000298 GO:0008486 GO:0034431 GO:0034432 GO:0046872 GO:0050072\n", | ||
"MF A0A075B6Q5 : GO:0003823 GO:0034987\n", | ||
"MF A0A075B6R2 : GO:0003823 GO:0034987\n", | ||
"CC A0A024RBG1 : GO:0005634 GO:0005737 GO:0005829\n", | ||
"CC A0A075B6H5 : GO:0005886\n", | ||
"CC A0A075B6H7 : GO:0005615 GO:0005886 GO:0019814\n", | ||
"BP A0A024RBG1 : GO:0071543 GO:1901907 GO:1901909 GO:1901911\n", | ||
"BP A0A075B6H5 : GO:0007166\n", | ||
"BP A0A075B6H7 : GO:0002250 GO:0002377 GO:0006955\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"for namespace, associations in ns2assc.items():\n", | ||
" for protein_id, go_ids in sorted(associations.items())[:3]:\n", | ||
" print(\"{NS} {PROT:7} : {GOs}\".format(\n", | ||
" NS=namespace,\n", | ||
" PROT=protein_id,\n", | ||
" GOs=' '.join(sorted(go_ids))))" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"# Bonus: The GPAD is stored as a list of named tuples\n", | ||
"The list of namedtuples is stored in the **GpadReader** data member named **_associations_**.\n", | ||
"\n", | ||
"Each namedtuple stores data for one line in the GPAD file." | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 6, | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"ntgpadobj(DB='UniProtKB', DB_ID='A0A024RBG1', Qualifier={'enables'}, GO_ID='GO:0046872', DB_Reference={'GO_REF:0000043'}, ECO='ECO:0000501', Evidence_Code='IEA', With_From={'UniProtKB-KW:KW-0479'}, Taxon=None, Date=datetime.date(2022, 9, 7), Assigned_By='UniProt', Extension=None, Properties={}, NS='MF')\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"# Sort the list of GPAD namedtuples by ID\n", | ||
"nts = sorted(anno.associations, key=lambda nt:nt.DB_ID)\n", | ||
"\n", | ||
"# Print one namedtuple\n", | ||
"print(nts[0])" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## Namedtuple fields\n", | ||
"```\n", | ||
"DB # 0 required 1 UniProtKB\n", | ||
"DB_ID # 1 required 1 P12345\n", | ||
"DB_Symbol # 2 required 1 PHO3\n", | ||
"Qualifier # 3 optional 0 or greater NOT\n", | ||
"GO_ID # 4 required 1 GO:0003993\n", | ||
"DB_Reference # 5 required 1 or greater PMID:2676709\n", | ||
"Evidence_Code # 6 required 1 IMP\n", | ||
"With_From # 7 optional 0 or greater GO:0000346\n", | ||
"Aspect # 8 required 1 F\n", | ||
"DB_Name # 9 optional 0 or 1 Toll-like receptor 4\n", | ||
"DB_Synonym # 10 optional 0 or greater hToll|Tollbooth\n", | ||
"DB_Type # 11 required 1 protein\n", | ||
"Taxon # 12 required 1 or 2 taxon:9606\n", | ||
"Date # 13 required 1 20090118\n", | ||
"Assigned_By # 14 required 1 SGD\n", | ||
"Annotation_Extension # 15 optional 0 or greater part_of(CL:0000576)\n", | ||
"Gene_Product_Form_ID # 16 optional 0 or 1 UniProtKB:P12345-2\n", | ||
"```" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"## Print a subset of the namedtuple fields" | ||
] | ||
}, | ||
{ | ||
"cell_type": "code", | ||
"execution_count": 7, | ||
"metadata": {}, | ||
"outputs": [ | ||
{ | ||
"name": "stdout", | ||
"output_type": "stream", | ||
"text": [ | ||
"MF A0A024RBG1 GO:0046872 IEA 2022-09-07 UniProt\n", | ||
"CC A0A024RBG1 GO:0005829 IDA 2016-12-04 HPA\n", | ||
"BP A0A024RBG1 GO:1901907 IBA 2017-02-28 GO_Central\n", | ||
"MF A0A024RBG1 GO:0000298 IBA 2017-02-28 GO_Central\n", | ||
"MF A0A024RBG1 GO:0008486 IBA 2021-05-30 GO_Central\n", | ||
"CC A0A024RBG1 GO:0005634 IBA 2017-02-28 GO_Central\n", | ||
"BP A0A024RBG1 GO:1901911 IBA 2017-02-28 GO_Central\n", | ||
"BP A0A024RBG1 GO:1901909 IBA 2017-02-28 GO_Central\n", | ||
"MF A0A024RBG1 GO:0034432 IBA 2017-02-28 GO_Central\n", | ||
"CC A0A024RBG1 GO:0005737 IBA 2017-02-28 GO_Central\n" | ||
] | ||
} | ||
], | ||
"source": [ | ||
"fmtpat = '{NS} {DB_ID} {GO_ID} {Evidence_Code} {Date} {Assigned_By}'\n", | ||
"for nt_line in nts[:10]:\n", | ||
" print(fmtpat.format(**nt_line._asdict()))" | ||
] | ||
}, | ||
{ | ||
"cell_type": "markdown", | ||
"metadata": {}, | ||
"source": [ | ||
"Copyright (C) 2010-present, DV Klopfenstein PhD, Haibao Tang. All rights reserved." | ||
] | ||
} | ||
], | ||
"metadata": { | ||
"kernelspec": { | ||
"display_name": "Python 3", | ||
"language": "python", | ||
"name": "python3" | ||
}, | ||
"language_info": { | ||
"codemirror_mode": { | ||
"name": "ipython", | ||
"version": 3 | ||
}, | ||
"file_extension": ".py", | ||
"mimetype": "text/x-python", | ||
"name": "python", | ||
"nbconvert_exporter": "python", | ||
"pygments_lexer": "ipython3", | ||
"version": "3.6.7" | ||
} | ||
}, | ||
"nbformat": 4, | ||
"nbformat_minor": 2 | ||
} |