def printClass(outStream, line):
outStream.write("<%s/%s> \n\ta owl:Class ;\n" % (visumpointGene.GO, line[1]))
outStream.write("\tVP:Symbol %s;\n" % (visumpointGene.symbol(visumpointGene.strip(line[2]))))
outStream.write("\tVP:Symbol %s;\n" % (visumpointGene.symbol(visumpointGene.strip(line[2]))))
# outStream.write('\trdfs:label "%s"^^xsd:string ;\n' % (visumpointGene.strip(line[2])))
# outStream.write('\trdfs:subClassOf VP:HUGO ;\n')
outStream.write(".\n\n")
def printFile(table, outfilename):
outStream = open(outfilename, "w")
# printHeader(outStream)
printHeader(outStream)
for item in table:
outStream.write("<%s/%s> \n\ta VP:GeneAnnotation ;\n" % (visumpointGene.GO, item))
outStream.write("\trdfs:subClassOf VP:GeneConcept ;\n")
for symbol in table[item]:
outStream.write("\tVP:GeneSymbol %s;\n" % (visumpointGene.symbol(visumpointGene.strip(symbol))))
for go in table[item][symbol]:
row = table[item][symbol][go]
outStream.write("%sVP:hasReference [\n" % ("\t"))
outStream.write("\t\ta\tVP:GO;\n")
outStream.write(
"\t\tVP:ID %s;\n" % (visumpointGene.urlGO(visumpointGene.strip("GO_" + go[3 : len(go)])))
)
if row[0].startswith("GO_REF"):
outStream.write(
"\t\tVP:GO_REF %s;\n"
% (visumpointGene.urlGO(visumpointGene.strip("GO_" + row[0][7 : len(row[0])])))
)
outStream.write("\t];\n")
outStream.write(".\n\n")
def printHUGOClass(outStream,line):
outStream.write('<%s/%s> \n\ta VP:HUGO ;\n' % (HUGO_NAMESPACE, (line[0])[5:len(line[0])]))
outStream.write('\trdfs:label "%s"^^xsd:string ;\n' % (stripStuff(line[2])))
#outStream.write('\trdfs:subClassOf VP:HUGO ;\n')
outStream.write('\tskos:prefLabel "%s"^^xsd:string ;\n' % (stripStuff(line[2])))
#outStream.write('\trdfs:subClassOf hugo:%s ;\n' % (line[0]))
#outStream.write('\thugo:Accession_Numbers BC022009"^^xsd:string ;\n')
outStream.write('\tVP:ApprovedName "%s"^^xsd:string ;\n' % (stripStuff(line[2])))
outStream.write('\tVP:ApprovedSymbol %s;\n' % (visumpointGene.symbol(visumpointGene.strip(line[1]))))
outStream.write('\tVP:ApprovedSymbolString "%s"^^xsd:string;\n' % (visumpointGene.strip(line[1])))
#outStream.write('\thugo:CCDS_IDs "CCDS31071.1"^^xsd:string;\n')
#outStream.write('\thugo:COSMIC_ID "RGS7"^^rdf:XMLLiteral ;\n')
#outStream.write('\thugo:COSMIC_LINK "<a href=\"http://www.sanger.ac.ukz/perl/genetics/CGP/cosmic?action=gene&ln=RGS7\">COSMIC</a>"^^rdf:XMLLiteral ;\n')
outStream.write('\tVP:Chromosome_Sym "%s"^^xsd:string ;\n' % (line[10]))
outStream.write('\tVP:Chromosome "%s"^^xsd:string;\n' % (line[10]))
outStream.write('\tSO:SO_0000105 %s;\n' % (getChromosome(line[10]))) # Chromosome Arm http://en.wikipedia.org/wiki/Locus_(genetics)
outStream.write('\tSO:SO_0000341 %s;\n' % (getChromosome(line[10]))) # Band
outStream.write('\tSO:SO_0000001 %s;\n' % (getChromosome(line[10]))) # Region
if len(line[11]) > 0:
outStream.write('\tVP:ApprovalDate "%s"^^xsd:date ;\n' % (line[11]))
if len(line[12]) > 0:
outStream.write('\tVP:DateModified "%s"^^xsd:date ;\n'% (line[12]))
if len(line[13]) > 0:
outStream.write('\tVP:DateSymbolChanged "%s"^^xsd:date ;\n' % (line[13]))
if len(line[14]) > 0:
outStream.write('\tVP:DateNameChanged "%s"^^xsd:date ;\n' % (line[14]))
#outStream.write('\thugo:Ensembl_ID__mapped_data_supplied_by_Ensembl "ENSG00000182901"^^xsd:string ;\n')
#outStream.write('\thugo:Entrez_Gene_ID "6000"^^xsd:string ;\n')
#outStream.write('\thugo:Entrez_Gene_ID__mapped_data_supplied_by_NCBI "6000"^^xsd:string ;\n')
#outStream.write('\thugo:GDB_ID__mapped_data "GDB:5912686"^^xsd:string ;\n')
#outStream.write('\thugo:Gene_Family_Tag "RGS"^^xsd:string ;\n')
#outStream.write('\thugo:HGNC_ID "HGNC:10003"^^xsd:string ;\n')
outStream.write('\tVP:hasLocusGroup %s;\n' % (LocusGroup(line[5])))
#outStream.write('\thugo:Locus_Specific_Databases "<strong></strong>"^^xsd:string ;\n')
outStream.write('\tVP:hasLocusType %s ;\n' % (LocusType(line[4])))
#outStream.write('\thugo:Mouse_Genome_Database_ID "MGI:1346089"^^xsd:string ;\n')
#outStream.write('\thugo:Mouse_Genome_Database_ID__mapped_data_supplied_by_MGI "MGI:1346089"^^xsd:string ;\n')
#outStream.write('\thugo:OMIM_ID__mapped_data_supplied_by_NCBI "602517"^^xsd:string ;\n')
if len(line[6]) > 0 :
for previousSymbol in line[6].split(','):
outStream.write('\tVP:PreviousSymbol %s ;\n ' % (visumpointGene.symbol(visumpointGene.strip(previousSymbol))))
outStream.write('\tVP:PreviousSymbolString \"%s\"^^xsd:string ;\n' % (stripStuff(previousSymbol)))
if len(line[7]) > 0 :
for previousNames in line[7].split(','):
outStream.write('\tVP:PreviousName \"%s\"^^xsd:string ;\n' % (stripStuff(previousNames)))
if len(line[8]) > 0 :
for synonyms in line[8].split(','):
outStream.write('\tVP:Synonym %s ;\n' % (visumpointGene.symbol(visumpointGene.strip(synonyms))))
outStream.write('\tVP:SynonymString \"%s\"^^xsd:string ;\n' % (stripStuff(synonyms)))
if len(line[22]) > 0 :
for pubmedID in line[22].split(','):
visumpointGene.printCitation(outStream,visumpointGene.PubMed,stripStuff(stripStuff(pubmedID)),"\t")
if len(line[23]) > 0 :
for RefSeq in line[23].split(','):
visumpointGene.printCrossReference(outStream,visumpointGene.RefSeq,stripStuff(RefSeq),"\t")
if len(line[34]) > 0 :
visumpointGene.printCrossReference(outStream,visumpointGene.RefSeq,stripStuff(line[34]),"\t")
if len(line[32]) > 0 :
for eg in line[32].split(','):
visumpointGene.printCrossReference(outStream,visumpointGene.Ensembl_ID,stripStuff(eg),"\t")
if len(line[15]) > 0 :
for an in line[15].split(','):
outStream.write('\tVP:hasAccessionNumber [\n')
outStream.write('\t\t\ta\tVP:AccessionNumber;\n')
outStream.write('\t\t\tVP:ID "%s"^^xsd:string;\n' % (an))
outStream.write('\t\t];\n')
if len(line[16]) > 0 :
visumpointGene.printCrossReference(outStream,visumpointGene.Enzyme_ID,stripStuff(line[16]),"\t")
if len(line[17]) > 0 :
visumpointGene.printCrossReference(outStream,visumpointGene.EntrezGene_ID,stripStuff(line[17]),"\t")
if len(line[18]) > 0 :
visumpointGene.printCrossReference(outStream,visumpointGene.Ensembl_ID,stripStuff(line[18]),"\t")
if len(line[19]) > 0 :
visumpointGene.printCrossReference(outStream,"MouseGenomeID",stripStuff(line[19]),"\t")
if len(line[29]) > 0 :
for an in line[29].split(','):
visumpointGene.printCrossReference(outStream,"CCSDID",stripStuff(an),"\t")
if len(line[30]) > 0 :
for an in line[30].split(','):
visumpointGene.printCrossReference(outStream,visumpointGene.Vega_ID,stripStuff(an),"\t")
if len(line[33]) > 0 :
visumpointGene.printCrossReference(outStream,visumpointGene.OMIM_ID,stripStuff(line[33]),"\t")
if len(line[36]) > 0 :
visumpointGene.printCrossReference(outStream,visumpointGene.Ensembl_ID,stripStuff(line[36]),"\t")
if len(line[37]) > 0 :
visumpointGene.printCrossReference(outStream,"UCSCID",stripStuff(line[37]),"\t")
if len(line[38]) > 0 :
visumpointGene.printCrossReference(outStream,"MouseGenomeID",stripStuff(line[38]),"\t")
if len(line[39]) > 0 :
visumpointGene.printCrossReference(outStream,"RatGenomeID",stripStuff(line[39]),"\t")
#outStream.write('\thugo:Rat_Genome_Database_ID__mapped_data_supplied_by_RGD "RGD:3570"^^xsd:string ;\n')
#outStream.write('\thugo:Record_Type "Standard"^^xsd:string ;\n')
#outStream.write('\thugo:RefSeq__mapped_data_supplied_by_NCBI "NM_002924"^^xsd:string ;\n')
outStream.write('\tVP:Status %s;\n' % (Status(line[3])))
#outStream.write('\thugo:UCSC_ID__mapped_data_supplied_by_UCSC "uc001hyv.2"^^xsd:string ;\n')
#outStream.write('\thugo:UniProt_ID__mapped_data_supplied_by_UniProt "P49802"^^xsd:string ;\n')
#outStream.write('\thugo:VEGA_IDs "OTTHUMG00000040107"^^xsd:string .\n')
outStream.write('.\n')
