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PharmGKB.py
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PharmGKB.py
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__author__ = 'lario'
import csv
import re
import regex
import os, urllib, datetime, time, sys
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")
DBSource = visumpointGene.VP_PharmGKB
Namespace = visumpointGene.URI_PharmGKB
def dbReference(inStr):
str = visumpointGene.strip(inStr.lower())
if str == "snomedct":
return visumpointGene.VP_SnoMedCT
if str == "umls":
return visumpointGene.VP_UMLS
if str == "ndfrt":
return visumpointGene.VP_NDFRT
if str == "meddra":
return visumpointGene.VP_MedDRA
if str == "mesh":
return visumpointGene.VP_Mesh
if str == "humancycgene":
return visumpointGene.VP_HumanCycGene
if str == "alfred":
return visumpointGene.VP_Alfred
if str == "ctd":
return visumpointGene.VP_CTD
if str == "ensembl":
return visumpointGene.VP_Ensembl
if str == "entrezgene":
return visumpointGene.VP_EntrezGene
if str == "genatlas":
return visumpointGene.VP_GenAtlas
if str == "genecard":
return visumpointGene.VP_GeneCard
if str == "go":
return visumpointGene.VP_GO
if str == "hgnc":
return visumpointGene.VP_HGNC
if str == "hugo":
return visumpointGene.VP_HUGO
if str == "huge":
return visumpointGene.VP_HUGE
if str == "dBase":
return visumpointGene.VP_DBase
if str == "hgnc":
return visumpointGene.VP_HGNC
if str == "hugo":
return visumpointGene.VP_HUGO
if str == "modbase":
return visumpointGene.VP_ModBas
if str == "mutdb":
return visumpointGene.VP_MutDb
if str.startswith("refseq"):
return visumpointGene.VP_RefSeq
if str == "omim":
return visumpointGene.VP_OMIM
if str == "uniprotkb":
return visumpointGene.VP_UniProtKb
if str == "ucscgenomebrowser":
return visumpointGene.VP_UCSCGenomeBrowser
if str == "iupharreceptor":
return visumpointGene.VP_IupharReceptor
if str == "url":
return visumpointGene.VP_URL
if str == "ttd":
return visumpointGene.VP_TTD
if str == "bindingdb":
return visumpointGene.VP_BindingDb
if str == "chemspider":
return visumpointGene.VP_ChemSpider
if str == "drugbank":
return visumpointGene.VP_DrugBank
if str == "keggcompound":
return visumpointGene.VP_KeggCompound
if str == "pubchemcompound":
return visumpointGene.VP_PubChemCompound
if str == "pubchemsubstance":
return visumpointGene.VP_SubChemSubstance
if str == "dailymed":
return visumpointGene.VP_DailyMed
if str == "het":
return visumpointGene.VP_HET
if str == "clinicaltrials":
return visumpointGene.VP_ClinicalTrials
if str == "dpd":
return visumpointGene.VP_DPD
if str == "chebi":
return visumpointGene.VP_Chebi
if str == "genbank":
return visumpointGene.VP_Genbank
if str == "ndc":
return visumpointGene.VP_NDC
if str == "iupharligand":
return visumpointGene.VP_Iupharligand
if str == "keggdrug":
return visumpointGene.VP_Keggdrug
if str == "pdb":
return visumpointGene.VP_PDB
if str == "refseqprot":
return visumpointGene.VP_RefSeqProt
return "ERROR %s" % inStr
def printRSIDClass(outStream,line):
outStream.write('<%s/%s>\n' % (Namespace, line[1]))
visumpointGene.printCrossReference(outStream,visumpointGene.VP_dbSNP,visumpointGene.strip(line[0]),visumpointGene.VP_PharmGKB,"\t\t")
outStream.write('\t. # %s %s\n\n' % (line[1], line[0]))
def printDrugClass(outStream,line, table):
drugName = visumpointGene.strip(line[1])
outStream.write('<%s/%s> \n\ta %s;\n' % (Namespace, line[0], visumpointGene.VP_PharmGKBDrug))
try :
outStream.write('\trdfs:label "%s"^^xsd:string ;\n' % (drugName))
if(len(line[7])):
outStream.write('\t%s %s;\n' % (visumpointGene.VP_SMILES, visumpointGene.smiles(line[7])))
if len(line[2]) > 0 :
for name in line[2].split(','):
visumpointGene.printGenericName(outStream, "", visumpointGene.strip(name), visumpointGene.VP_PharmGKB,"\t")
if len(line[3]) > 0 :
for name in line[2].split(','):
visumpointGene.printTradeName(outStream, "", visumpointGene.strip(name), visumpointGene.VP_PharmGKB,"\t")
try:
if len(line[6]) > 0 :
for xref in line[6].split(','):
try :
db = xref.split(":")[0]
if db == "go":
id = xref.split(":")[2]
elif db =="url":
id = xref.split(":")[1] + ":" + xref.split(":")[2]
else:
id = xref.split(":")[1]
visumpointGene.printCrossReference(outStream,dbReference(db),visumpointGene.strip(id),visumpointGene.VP_PharmGKB, "\t")
except :
outStream.write('# ERROR PROCESSING printDrugClass - %s %s %s\n\n' % (line[1], line[0], xref))
except:
outStream.write('# ERROR PROCESSING printDrugClass - %s %s\n\n' % (line[1], line[0]))
if drugName in table:
for gene in table[drugName]:
if not gene == NO_GENE:
visumpointGene.printHasGeneRelationship(outStream, visumpointGene.VP_Unknown , visumpointGene.strip(gene), visumpointGene.VP_PharmGKB,"\t")
except:
outStream.write('# ERROR PROCESSING printDrugClass - %s %s\n\n' % (line[1], line[0]))
outStream.write('\t. # %s %s\n\n' % (line[1], line[0]))
#printDiseaseClass
def printDiseaseClass(outStream,line):
outStream.write('<%s/%s> \n\ta %s;\n' % (Namespace, line[0], visumpointGene.VP_PharmGKBDisease))
outStream.write('\trdfs:label "%s"^^xsd:string ;\n' % (visumpointGene.strip(line[1])))
outStream.write('\tskos:prefLabel "%s"^^xsd:string ;\n' % (visumpointGene.strip(line[1])))
trip = ""
useName = ""
if len(line[2]) > 0 :
for name in line[2].split(','):
if name.startswith("\"") and name.endswith("\""):
useName = name
elif name.startswith("\""):
trip = name
elif name.endswith("\""):
useName = (trip + "," +name).strip("\"")
trip = ""
else :
useName = name
if len(useName) > 0:
visumpointGene.printAlternativeName(outStream, "", visumpointGene.strip(useName), visumpointGene.VP_PharmGKB,"\t\t")
useName = ""
db_id_type_strB = "(.+):(.+)\((.+)\[(.+)/(.+)\]"
db_id_PP = r'(.+):(.+)\(([^()]++)\((.*)\)+'
strExp = "(.+):(.+)\((.+)"
if len(line[4]) > 0 :
for name in line[4].split('),'):
#db_id_type_strB = "(.+):(.+)\((.+)\[(.+)/(.+)\]"
try:
match = regex.match(db_id_type_strB, name, regex.M|regex.I)
if (match):
visumpointGene.printCrossReference(outStream, dbReference(match.group(1)), visumpointGene.strip(match.group(2)), visumpointGene.VP_PharmGKB,"\t\t")
else :
#db_id_PP = r'(.+):(.+)\(([^()]++)\((.*)\)+'
try:
match1 = regex.match( db_id_PP, name, re.M|re.I)
if (match1):
visumpointGene.printCrossReference(outStream, dbReference(match1.group(1)), visumpointGene.strip(match1.group(2)), visumpointGene.VP_PharmGKB,"\t\t")
else :
#strExp = "(.+):(.+)\((.+)"
try:
match2 = regex.match( strExp, name, re.M|re.I)
if(match2):
visumpointGene.printCrossReference(outStream, dbReference(match2.group(1)), visumpointGene.strip(match2.group(2)), visumpointGene.VP_PharmGKB,"\t\t")
else :
outStream.write("#ERROR : processing External References : %s\n" % name)
outStream.write("#\t\t %s\n" % line[4])
except:
e = sys.exc_info()[0]
print( "Error: %s" % e )
except:
e = sys.exc_info()[0]
print( "Error: %s" % e )
except:
e = sys.exc_info()[0]
print( "Error: %s" % e )
outStream.write('\t. # %s %s\n\n' % (line[1], line[0]))
def printGeneClass(outStream,line):
outStream.write('<%s/%s> \n\ta %s;\n' % (Namespace, line[0], visumpointGene.VP_PharmGKBGene))
outStream.write('\trdfs:label "%s"^^xsd:string ;\n' % (visumpointGene.strip(line[3])))
visumpointGene.printCrossReference(outStream, visumpointGene.EntrezGene_ID , visumpointGene.strip(line[1]), visumpointGene.VP_PharmGKB, "\t\t")
visumpointGene.printCrossReference(outStream, visumpointGene.Ensembl_ID , visumpointGene.strip(line[2]), visumpointGene.VP_PharmGKB, "\t\t")
visumpointGene.printHasSymbol(outStream, visumpointGene.Ensembl_ID , visumpointGene.strip(line[4]), visumpointGene.VP_PharmGKB,"\t\t")
try:
if line[0] == "PA134868213":
x = 0
if len(line[10]) and line[10] != 'null' :
outStream.write('\tVP:CPIC "%s"^^xsd:boolean ;\n' % (visumpointGene.trueFalse(visumpointGene.strip(line[10]))))
if len(line[11]) > 0 and line[11] != 'null' :
outStream.write('\tVP:Chromosome "%s"^^xsd:string;\n' % (visumpointGene.strip(line[11])))
if len(line[12]) > 0 and line[12] != 'null' :
outStream.write('\tVP:Start "%s"^^xsd:integer;\n' % (visumpointGene.strip(line[12])))
if len(line[13]) > 0 and line[13] != 'null' :
outStream.write('\tVP:End "%s"^^xsd:integer ;\n' % (visumpointGene.strip(line[13])))
except:
outStream.write('# Error XREF %s\n\n\n' % (line[0]))
try:
if len(line[9]) > 0 :
for xref in line[9].split(','):
db =""
id = ""
try:
db = xref.split(":")[0]
if db == "go":
id = xref.split(":")[2]
elif db =="url":
id = xref.split(":")[1] + ":" + xref.split(":")[2]
else:
id = xref.split(":")[1]
if len(db) > 0 and len(id) > 0:
visumpointGene.printCrossReference(outStream,dbReference(visumpointGene.strip(db)),visumpointGene.strip(id),visumpointGene.VP_PharmGKB, "\t\t")
except:
outStream.write('#Error XREF -> %s - %s\n\n\n' % (line[0], xref))
except:
outStream.write('# Error XREF %s\n\n\n' % (line[0]))
#outStream.write('\t\t\t # %s\n' % (visumpointGene.strip(xref)))
outStream.write('\t. # %s\n\n\n' % (line[0]))
def readDrugsFile(infilename, outStream, table):
x = 0
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
if x > START:
print("Disease : %s - %s" % (x,line[0]))
try:
printDrugClass(outStream,line, table)
except:
print("ERROR ON ROW - readDrugsFile : %s - %s" % (x,line[0]))
outStream.write("\n# ERROR ON ROW: %s - PharmGKB ID : %s\n\n" % (x,line[0]))
if x > END:
return
x = x + 1
except:
print("ERROR ON ROW - readDrugsFile")
e = sys.exc_info()[0]
print( "Error: %s" % e )
finally:
f.close()
return
NO_GENE = "NO_GENE"
def readDrugLabelsFile(infilename):
drug = ""
genes = ""
x = 0
table = {}
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
if x > START:
print("Drug Labels : %s - %s" % (x,line[1]))
try:
match = regex.match(r'FDA Label for ([a-zA-Z0-9 \-,]+) and (.+)', line[1], regex.M|regex.I)
if not match:
match = regex.match(r'European Medicines Agency \(EMA\) Label for ([a-zA-Z0-9 \-,]+) and (.+)', line[1], regex.M|regex.I)
if(match):
drug = match.group(1)
genes = match.group(2)
else :
match = regex.match(r'FDA Label for ([a-zA-Z0-9 \-,]+)', line[1], regex.M|regex.I)
if not match:
match = regex.match(r'European Medicines Agency \(EMA\) Label for ([a-zA-Z0-9 \-,]+)', line[1], regex.M|regex.I)
if (match):
drug = match.group(1)
genes = ""
else:
print("ERROR ON ROW - readDrugLabelsFile : %s - %s" % (line[1]))
if len(drug) > 0:
if drug in table:
row = table[drug]
else:
row = {}
table[drug] = row
if(len(genes) > 0):
for gene in genes.split(","):
row[gene] = {gene, line[2], line[3],line[4]}
else :
row[NO_GENE] = {NO_GENE, line[2], line[3],line[4]}
drug = ""
genes = ""
except:
print("ERROR ON ROW - readDrugLabelsFile 2: %s - %s" % (x,line[0]))
if x > END:
return table
x = x + 1
finally:
f.close()
return table
def readDiseasesFile(infilename, outStream):
x = 0
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
if x > START:
print("Disease : %s - %s" % (x,line[0]))
try:
printDiseaseClass(outStream,line)
except:
print("ERROR ON ROW - readDiseasesFile: %s - %s" % (x,line[0]))
outStream.write("\n# ERROR ON ROW - readDiseasesFile: %s - PharmGKB ID : %s\n\n" % (x,line[0]))
if x > END:
return
x = x + 1
except:
print("ERROR ON ROW - readDiseasesFile")
finally:
f.close()
return
def readRSIFFile(infilename, outStream):
x = 0
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
if x > START+1:
print("RSID : %s - %s" % (x,line[0]))
try:
printRSIDClass(outStream,line)
except:
print("ERROR ON ROW - readRSIFFile: %s - %s" % (x,line[1]))
outStream.write("\n# ERROR ON ROW - readRSIFFile: %s - PharmGKB ID : %s\n\n" % (x,line[1]))
if x > END:
return
x = x + 1
finally:
f.close()
return
def readGeneFile(infilename, outStream):
x = 0
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
if x > START:
print("GENE : %s - %s" % (x,line[0]))
try:
printGeneClass(outStream,line)
except:
print("ERROR ON ROW - readGeneFile: %s - %s" % (x,line[0]))
outStream.write("\n# ERROR ON ROW - readGeneFile: %s - PharmGKB ID : %s\n\n" % (x,line[0]))
if x > END:
return
x = x + 1
finally:
f.close()
return
def readFiles(dir, ttlFile):
#ttlFile = "D:/My Workspaces/EmptyTest/visumpoint/140815/PharmGKB.ttl"
#dir = "D:/My Ontologies/PharmGKB/140815"
geneFile = "%s/%s" % (dir, "genes.tsv")
rsidFile = "%s/%s" % (dir, "rsid.tsv")
diseaseFile = "%s/%s" % (dir, "diseases.tsv")
drugsFile = "%s/%s" % (dir, "drugs.tsv")
drugLabelsFile = "%s/%s" % (dir, "drugLabels.tsv")
try:
outStream = open(ttlFile, 'w')
printHeader(outStream)
table = readDrugLabelsFile(drugLabelsFile)
readGeneFile(geneFile, outStream)
readRSIFFile(rsidFile, outStream)
readDiseasesFile(diseaseFile, outStream)
readDrugsFile(drugsFile, outStream, table)
x = 0
finally:
outStream.close()
START = 0
END = 20000000000
def main():
readFiles("D:/My Ontologies/PharmGKB/140815","D:/My Workspaces/EmptyTest/visumpoint/140815/PharmGKB.ttl" )
str = "NDFRT:N0000002071(Mycobacterium Infections [Disease/Finding])"
str1 = "MeSH:D015430(Weight Gain)"
str2 = "SnoMedCT:109978004(T-cell lymphoma (clinical)"
str3 = "MeSH:D016399(Lymphoma, T-Cell)"
str4 = "MeSH:D015430(Weight Gain"
#match = re.match( r'(.+):(.+)\((.+)\)', str, re.M|re.I)
match = re.match( r'(.+):(.+)[\(+](.+)[\)+]', str3, re.M|re.I)
#match = re.match( r'(.+):(.+)[\(+](.+)[\(*](.+)[\)+][\)*]', str2, re.M|re.I)
match = re.match( r'(.+):(.+)[\(+](.+)[\(*](.*)[\)*]', str2, re.M|re.I)
#match = re.match( r'(.+):(.+)[\(+](.+)([\(*].+[\)*])[\)+]', str3, re.M|re.I)
#match = re.match( r'(.+):(.+)\(+(.+)\)', str2, re.M|re.I)
if match:
print "matchObj.group() : ", match.group()
print "matchObj.group(1) : ", match.group(1)
print "matchObj.group(2) : ", match.group(2)
print "matchObj.group(3) : ", match.group(3)
#print "matchObj.group(4) : ", match.group(4)
else:
print "No match!!"
db_id_type_strB = "(.+):(.+)\((.+)\[(.+)/(.+)\]"
db_id_PP = r'(.+):(.+)\(([^()]++)\((.*)\)+'
strExp = "(.+):(.+)\((.+)"
def test():
s = 'aaa(((1+0)+1)+1)bbb'
db_id_type_str = r'(.+):(.+)\((.+)'
str1 = "NDFRT:N0000002071(Mycobacterium Infections [Disease/Finding])"
db_id_type_strB = "(.+):(.+)\((.+)\[(.+)/(.+)\]"
str2 = "SnoMedCT:109978004(T-cell lymphoma (clinical)"
db_id_PP = r'(.+):(.+)\(([^()]++)\((.*)\)+'
str3 = "MeSH:D015430(Weight Gain"
strExp = "(.+):(.+)\((.+)"
str4 = "MeSH:D015430(Weight Gain"
match = regex.match(db_id_PP, str4, regex.M|regex.I)
if match:
print "matchObj.group() : ", match.group()
print "matchObj.group(1) : ", match.group(1)
print "matchObj.group(2) : ", match.group(2)
print "matchObj.group(3) : ", match.group(3)
print "matchObj.group(4) : ", match.group(4)
print "matchObj.group(5) : ", match.group(5)
else:
print "No match!!"
def test2() :
str = 'Achromatopsia,"Acquired Color Blindness","Blindness, Color","Blue Color Blindness","Color Blindness","Color Blindness, Acquired","Color Blindness, Blue","Color Blindness, Green","Color Blindness, Inherited","Color Blindness, Red","Color Blindness, Red Green","Color Blindness, Red-Green","Color Vision Defect","Defect, Color Vision","Defect, Deutan","Defects, Color Vision","Deutan Defect","Green Color Blindness","Inherited Color Blindness","Monochromatopsia","Protan Defect","Red Color Blindness","Red-Green Color Blindness","Tritan Defect","Vision Defect, Color","Vision Defects, Color",'
pattern = regex.compile(r'\"*[a-zA-Z ]+\"*')
for (drug) in regex.findall(pattern, str):
print drug
#print numbers, '*', letters
def test3() :
str = 'Achromatopsia,"test","Acquired Color Blindness","Blindness, Color","Blue Color Blindness","Color Blindness","Color Blindness, Acquired","Color Blindness, Blue","Color Blindness, Green","Color Blindness, Inherited","Color Blindness, Red","Color Blindness, Red Green","Color Blindness, Red-Green","Color Vision Defect","Defect, Color Vision","Defect, Deutan","Defects, Color Vision","Deutan Defect","Green Color Blindness","Inherited Color Blindness","Monochromatopsia","Protan Defect","Red Color Blindness","Red-Green Color Blindness","Tritan Defect","Vision Defect, Color","Vision Defects, Color",'
str = 'Grafting,NOS,"Transplant procedure","Transplantation - action","Tx - Transplant",'
trip = ""
for name in str.split(','):
if name.startswith("\"") and name.endswith("\""):
useName = name
elif name.startswith("\""):
trip = name
elif name.endswith("\""):
useName = (trip + "," +name).strip("\"")
trip = ""
else :
useName = name
if len(useName) > 0:
print useName.strip("\"")
useName = ""
def TestreadDrugsFile(infilename):
x = 0
try:
with open(infilename, 'r') as f:
lineRaw = csv.reader(f, delimiter='\t', quoting=csv.QUOTE_NONE)
for line in lineRaw:
print "Row %s - %s OK" % (x, line[0])
x = x + 1
except:
print("Row %s FAILED!" % (x))
e = sys.exc_info()
print( "Error: %s - %s -%s" % (e[0], e[1], e[2]))
finally:
f.close()
return
#TestreadDrugsFile("D:/My Ontologies/PharmGKB/140815/drugs2.tsv")
main()