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GOAnnotation.py
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GOAnnotation.py
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__author__ = 'lario'
import csv
import re
import visumpointGene
def printHeader(outStream):
#outStream.write("@prefix %s: <%s#> .\n\n" % (visumpointGene.VP , MAIN_NAMESPACE))
outStream.write("@prefix VP: <%s/> .\n" % (visumpointGene.VP))
outStream.write("@prefix skos: <http://www.w3.org/2004/02/skos/core#> .\n")
outStream.write("@prefix owl: <http://www.w3.org/2002/07/owl#> .\n")
outStream.write("@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .\n")
outStream.write("@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .\n")
outStream.write("@prefix umls: <http://bioportal.bioontology.org/ontologies/umls/> .\n")
outStream.write("@prefix GO: <%s/> .\n" % (visumpointGene.GO))
outStream.write("@prefix PMID: <http://purl.obolibrary.org/obo/> .\n")
outStream.write("@prefix vtw-cpt: <http://www.omg.org/spec/VTW/Concepts/>.\n")
outStream.write("\n\n")
def buildTable(infilename, outfilename):
x = 0
outStream = open(outfilename, 'w')
#printHeader(outStream)
table = {}
item = ""
symbol = ""
go = ""
printHeader(outStream)
print(outfilename)
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
if not line[0].startswith("!") and not line[0].startswith("\""):
item = line[1]
symbol = line[2]
go = line[4]
if not item in table :
table[item] = {}
if not symbol in table[item] :
table[item][symbol] = {}
if not go in table[item][symbol] :
table[item][symbol][go] = [line[5],line[6],line[7],line[8],line[9],line[10],line[11],line[12],line[13]]
x = x + 1
if x > 30000000 :
return table
print(x)
finally:
f.close()
outStream.close()
return table
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 readFile(infilename, outfilename):
x = 0
outStream = open(outfilename, 'w')
#printHeader(outStream)
printHeader(outStream)
print(outfilename)
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
if not line[0].startswith("!"):
if x < 1000000:
print(line[1])
printClass(outStream,line)
x = x + 1
if x > 10:
return
finally:
f.close()
outStream.close()
return
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 main(inFile = "D:/My Ontologies/GO/gene_association.goa_human", outfile = "D:/My Workspaces/EmptyTest/visumpoint/140815/GoAnnotationHuman.ttl"):
table = buildTable(inFile ,outfile)
printFile(table,outfile)
main()