#!/usr/bin/env python # Copyright 2013, 2016 by Iddo Friedberg idoerg@gmail.com. All rights reserved. # Copyright 2020 by Sergio Valqui. All rights reserved. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Parsers for the GAF, GPA and GPI formats from UniProt-GOA. Uniprot-GOA README + GAF format description: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/README Gene Association File, GAF formats: http://geneontology.org/docs/go-annotation-file-gaf-format-2.2/ http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/ http://geneontology.org/docs/go-annotation-file-gaf-format-2.0/ Gene Product Association Data (GPA format) README: http://geneontology.org/docs/gene-product-association-data-gpad-format/ Gene Product Information (GPI format) README: http://geneontology.org/docs/gene-product-information-gpi-format/ Go Annotation files are located here: ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ """ import copy # GAF: GO Annotation Format # # GAF version 2.0 GAF20FIELDS = [ "DB", "DB_Object_ID", "DB_Object_Symbol", "Qualifier", "GO_ID", "DB:Reference", "Evidence", "With", "Aspect", "DB_Object_Name", "Synonym", "DB_Object_Type", "Taxon_ID", "Date", "Assigned_By", "Annotation_Extension", "Gene_Product_Form_ID", ] # GAF version 1.0 GAF10FIELDS = [ "DB", "DB_Object_ID", "DB_Object_Symbol", "Qualifier", "GO_ID", "DB:Reference", "Evidence", "With", "Aspect", "DB_Object_Name", "Synonym", "DB_Object_Type", "Taxon_ID", "Date", "Assigned_By", ] # GPA version 1.0 GPA10FIELDS = [ "DB", "DB_Object_ID", "Qualifier", "GO_ID", "DB:Reference", "Evidence code", "With", "Interacting_taxon_ID", "Date", "Assigned_by", "Annotation_Extension", "Spliceform_ID", ] # GPA version 1.1 GPA11FIELDS = [ "DB", "DB_Object_ID", "Qualifier", "GO_ID", "DB:Reference", "ECO_Evidence_code", "With", "Interacting_taxon_ID", "Date", "Assigned_by", "Annotation Extension", "Annotation_Properties", ] # GPI version 1.0 GPI10FIELDS = [ "DB", "DB_subset", "DB_Object_ID", "DB_Object_Symbol", "DB_Object_Name", "DB_Object_Synonym", "DB_Object_Type", "Taxon", "Annotation_Target_Set", "Annotation_Completed", "Parent_Object_ID", ] # GPI version 1.1 GPI11FIELDS = [ "DB_Object_ID", "DB_Object_Symbol", "DB_Object_Name", "DB_Object_Synonym", "DB_Object_Type", "Taxon", "Parent_Object_ID", "DB_Xref", "Gene_Product_Properties", ] # GPI version 1.2 GPI12FIELDS = [ "DB", "DB_Object_ID", "DB_Object_Symbol", "DB_Object_Name", "DB_Object_Synonym", "DB_Object_Type", "Taxon", "Parent_Object_ID", "DB_Xref", "Gene_Product_Properties", ] def _gpi10iterator(handle): """Read GPI 1.0 format files (PRIVATE). This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.0 format. """ for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[5] = inrec[5].split("|") # DB_Object_Synonym(s) inrec[8] = inrec[8].split("|") # Annotation_Target_Set yield dict(zip(GPI10FIELDS, inrec)) def _gpi11iterator(handle): """Read GPI 1.1 format files (PRIVATE). This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.1 format. """ for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[2] = inrec[2].split("|") # DB_Object_Name inrec[3] = inrec[3].split("|") # DB_Object_Synonym(s) inrec[7] = inrec[7].split("|") # DB_Xref(s) inrec[8] = inrec[8].split("|") # Properties yield dict(zip(GPI11FIELDS, inrec)) def _gpi12iterator(handle): """Read GPI 1.2 format files (PRIVATE). This iterator is used to read a gp_information.goa_uniprot file which is in the GPI 1.2 format. """ for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[3] = inrec[3].split("|") # DB_Object_Name inrec[4] = inrec[4].split("|") # DB_Object_Synonym(s) inrec[8] = inrec[8].split("|") # DB_Xref(s) inrec[9] = inrec[9].split("|") # Properties yield dict(zip(GPI12FIELDS, inrec)) def gpi_iterator(handle): """Read GPI format files. This function should be called to read a gp_information.goa_uniprot file. At the moment, there is only one format, but this may change, so this function is a placeholder a future wrapper. """ inline = handle.readline() if inline.strip() == "!gpi-version: 1.2": return _gpi12iterator(handle) elif inline.strip() == "!gpi-version: 1.1": # sys.stderr.write("gpi 1.1\n") return _gpi11iterator(handle) elif inline.strip() == "!gpi-version: 1.0": # sys.stderr.write("gpi 1.0\n") return _gpi10iterator(handle) elif inline.strip() == "!gpi-version: 2.1": # sys.stderr.write("gpi 2.1\n") # return _gpi20iterator(handle) raise NotImplementedError("Sorry, parsing GPI version 2 not implemented yet.") else: raise ValueError(f"Unknown GPI version {inline}\n") def _gpa10iterator(handle): """Read GPA 1.0 format files (PRIVATE). This iterator is used to read a gp_association.* file which is in the GPA 1.0 format. Do not call directly. Rather, use the gpaiterator function. """ for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[2] = inrec[2].split("|") # Qualifier inrec[4] = inrec[4].split("|") # DB:Reference(s) inrec[6] = inrec[6].split("|") # With inrec[10] = inrec[10].split("|") # Annotation extension yield dict(zip(GPA10FIELDS, inrec)) def _gpa11iterator(handle): """Read GPA 1.1 format files (PRIVATE). This iterator is used to read a gp_association.goa_uniprot file which is in the GPA 1.1 format. Do not call directly. Rather use the gpa_iterator function """ for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[2] = inrec[2].split("|") # Qualifier inrec[4] = inrec[4].split("|") # DB:Reference(s) inrec[6] = inrec[6].split("|") # With inrec[10] = inrec[10].split("|") # Annotation extension yield dict(zip(GPA11FIELDS, inrec)) def gpa_iterator(handle): """Read GPA format files. This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gpa 1.1 or a gpa 1.0 iterator as needed """ inline = handle.readline() if inline.strip() == "!gpa-version: 1.1": # sys.stderr.write("gpa 1.1\n") return _gpa11iterator(handle) elif inline.strip() == "!gpa-version: 1.0": # sys.stderr.write("gpa 1.0\n") return _gpa10iterator(handle) else: raise ValueError(f"Unknown GPA version {inline}\n") def _gaf20iterator(handle): for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[3] = inrec[3].split("|") # Qualifier inrec[5] = inrec[5].split("|") # DB:reference(s) inrec[7] = inrec[7].split("|") # With || From inrec[10] = inrec[10].split("|") # Synonym inrec[12] = inrec[12].split("|") # Taxon yield dict(zip(GAF20FIELDS, inrec)) def _gaf10iterator(handle): for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[3] = inrec[3].split("|") # Qualifier inrec[5] = inrec[5].split("|") # DB:reference(s) inrec[7] = inrec[7].split("|") # With || From inrec[10] = inrec[10].split("|") # Synonym inrec[12] = inrec[12].split("|") # Taxon yield dict(zip(GAF10FIELDS, inrec)) def _gaf10byproteiniterator(handle): cur_id = None id_rec_list = [] for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[3] = inrec[3].split("|") # Qualifier inrec[5] = inrec[5].split("|") # DB:reference(s) inrec[7] = inrec[7].split("|") # With || From inrec[10] = inrec[10].split("|") # Synonym inrec[12] = inrec[12].split("|") # Taxon cur_rec = dict(zip(GAF10FIELDS, inrec)) if cur_rec["DB_Object_ID"] != cur_id and cur_id: ret_list = copy.copy(id_rec_list) id_rec_list = [cur_rec] cur_id = cur_rec["DB_Object_ID"] yield ret_list else: cur_id = cur_rec["DB_Object_ID"] id_rec_list.append(cur_rec) def _gaf20byproteiniterator(handle): cur_id = None id_rec_list = [] for inline in handle: if inline[0] == "!": continue inrec = inline.rstrip("\n").split("\t") if len(inrec) == 1: continue inrec[3] = inrec[3].split("|") # Qualifier inrec[5] = inrec[5].split("|") # DB:reference(s) inrec[7] = inrec[7].split("|") # With || From inrec[10] = inrec[10].split("|") # Synonym inrec[12] = inrec[12].split("|") # Taxon cur_rec = dict(zip(GAF20FIELDS, inrec)) if cur_rec["DB_Object_ID"] != cur_id and cur_id: ret_list = copy.copy(id_rec_list) id_rec_list = [cur_rec] cur_id = cur_rec["DB_Object_ID"] yield ret_list else: cur_id = cur_rec["DB_Object_ID"] id_rec_list.append(cur_rec) def gafbyproteiniterator(handle): """Iterate over records in a gene association file. Returns a list of all consecutive records with the same DB_Object_ID This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gaf 2.0 or a gaf 1.0 iterator as needed 2016-04-09: added GAF 2.1 iterator & fixed bug in iterator assignment In the meantime GAF 2.1 uses the GAF 2.0 iterator """ inline = handle.readline() if inline.strip() == "!gaf-version: 2.0": # sys.stderr.write("gaf 2.0\n") return _gaf20byproteiniterator(handle) elif inline.strip() == "!gaf-version: 1.0": # sys.stderr.write("gaf 1.0\n") return _gaf10byproteiniterator(handle) elif inline.strip() == "!gaf-version: 2.1": # Handle GAF 2.1 as GAF 2.0 for now TODO: fix # sys.stderr.write("gaf 2.1\n") return _gaf20byproteiniterator(handle) elif inline.strip() == "!gaf-version: 2.2": # Handle GAF 2.2 as GAF 2.0 for now. Change from # 2.1 to 2.2 is that Qualifier field is no longer optional. # As this type of checks has not been done before, we can # continue to use the gaf2.0 parser return _gaf20byproteiniterator(handle) else: raise ValueError(f"Unknown GAF version {inline}\n") def gafiterator(handle): """Iterate over a GAF 1.0 or 2.x file. This function should be called to read a gene_association.goa_uniprot file. Reads the first record and returns a gaf 2.x or a gaf 1.0 iterator as needed Example: open, read, interat and filter results. Original data file has been trimmed to ~600 rows. Original source ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/YEAST/goa_yeast.gaf.gz >>> from Bio.UniProt.GOA import gafiterator, record_has >>> Evidence = {'Evidence': set(['ND'])} >>> Synonym = {'Synonym': set(['YA19A_YEAST', 'YAL019W-A'])} >>> Taxon_ID = {'Taxon_ID': set(['taxon:559292'])} >>> with open('UniProt/goa_yeast.gaf', 'r') as handle: ... for rec in gafiterator(handle): ... if record_has(rec, Taxon_ID) and record_has(rec, Evidence) and record_has(rec, Synonym): ... for key in ('DB_Object_Name', 'Evidence', 'Synonym', 'Taxon_ID'): ... print(rec[key]) ... Putative uncharacterized protein YAL019W-A ND ['YA19A_YEAST', 'YAL019W-A'] ['taxon:559292'] Putative uncharacterized protein YAL019W-A ND ['YA19A_YEAST', 'YAL019W-A'] ['taxon:559292'] Putative uncharacterized protein YAL019W-A ND ['YA19A_YEAST', 'YAL019W-A'] ['taxon:559292'] """ inline = handle.readline() if inline.strip() == "!gaf-version: 2.0": # sys.stderr.write("gaf 2.0\n") return _gaf20iterator(handle) elif inline.strip() == "!gaf-version: 2.1": # sys.stderr.write("gaf 2.1\n") # Handle GAF 2.1 as GAF 2.0 for now. TODO: fix return _gaf20iterator(handle) elif inline.strip() == "!gaf-version: 2.2": # Handle GAF 2.2 as GAF 2.0 for now. Change from # 2.1 to 2.2 is that Qualifier field is no longer optional. # As this type of checks has not been done before, we can # continue to use the gaf2.0 parser return _gaf20iterator(handle) elif inline.strip() == "!gaf-version: 1.0": # sys.stderr.write("gaf 1.0\n") return _gaf10iterator(handle) else: raise ValueError(f"Unknown GAF version {inline}\n") def writerec(outrec, handle, fields=GAF20FIELDS): """Write a single UniProt-GOA record to an output stream. Caller should know the format version. Default: gaf-2.0 If header has a value, then it is assumed this is the first record, a header is written. """ outstr = "" for field in fields[:-1]: if isinstance(outrec[field], list): for subfield in outrec[field]: outstr += subfield + "|" outstr = outstr[:-1] + "\t" else: outstr += outrec[field] + "\t" outstr += outrec[fields[-1]] + "\n" handle.write(outstr) def writebyproteinrec(outprotrec, handle, fields=GAF20FIELDS): """Write a list of GAF records to an output stream. Caller should know the format version. Default: gaf-2.0 If header has a value, then it is assumed this is the first record, a header is written. Typically the list is the one read by fafbyproteinrec, which contains all consecutive lines with the same DB_Object_ID """ for outrec in outprotrec: writerec(outrec, handle, fields=fields) def record_has(inrec, fieldvals): """Accept a record, and a dictionary of field values. The format is {'field_name': set([val1, val2])}. If any field in the record has a matching value, the function returns True. Otherwise, returns False. """ retval = False for field in fieldvals: if isinstance(inrec[field], str): set1 = {inrec[field]} else: set1 = set(inrec[field]) if set1 & fieldvals[field]: retval = True break return retval if __name__ == "__main__": from Bio._utils import run_doctest run_doctest(verbose=0)