def fieldDic(record, fields):
dic = {}
vcf = commonTool.vcf(record)
for field in fields:
value = vcf.parseInfo(field)
dic[field] = value
return dic
def splitVcf(infile, outfile, fields):
infile = open(infile, 'r')
outfile = open(outfile, 'w')
fields = fields.split(",")
outfile.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n")
for line in infile:
if not line.startswith("#"):
record = line.split("\t")
dic = fieldDic(record, fields)
vcf = commonTool.vcf(record)
if not "," in record[4]:
output = record[0:7]
info = ""
for field in fields:
info += "%s=%s;" % (field, dic[field])
info = info.strip(";")
output.append(info)
outfile.write("\t".join(output))
outfile.write("\n")
else:
altAlleles = record[4].split(",")
n = 0
while n < len(altAlleles):
output = record[0:4] + [altAlleles[n]] + record[5:7]
info = ""
for field in fields:
if "," in dic[field]:
info += "%s=%s;" % (field,
dic[field].split(",")[n])
else:
info += "%s=%s;" % (field, dic[field])
info = info.strip(";")
output.append(info)
newVcf = commonTool.vcf(output)
outputLeft = newVcf.leftAlign()
outfile.write("\t".join(outputLeft))
outfile.write("\n")
n += 1
infile.close()
outfile.close()
def parseIlluminaNextseq(infile, outfile):
infile = open(infile, 'r')
outfile = open(outfile, 'w')
for line in infile:
if not line.startswith("#"):
record = line.split("\t")
if len(record[3]) == len(record[4]):
type = "snv"
else:
type = "indel"
vcf = commonTool.vcf(record)
readDepth = vcf.parseInfo("DP")
altFreq = str(float(vcf.parseDetail("VF", 10)) * 100)
alleleDepth = vcf.parseDetail("AD", 10)
altDepth = alleleDepth.split(
",")[1].rstrip() #removes the newline character
vep = vcf.parseInfo("CSQ").split('|')
#print vep
#parse dbsnp and cosmic from vep field
#CSQ=G|intron_variant|MODIFIER|CSF3R|ENSG00000119535|Transcript|ENST00000373103|protein_coding||15/16|ENST00000373103.1:c.1959-107T>C|||||||||-1|HGNC|2439||||||||||||| GT:GQ:AD:VF:NL:SB:GQX 0/1:59:827,26:0.0304:20:-30.0099:59
#CSQ=-|intron_variant|MODIFIER|UBE2N|ENSG00000177889|Transcript|ENST00000318066|protein_coding||1/3|ENST00000318066.2:c.30+3207delc|||||||||-1|HGNC|12492||||||||||||| GT:VF:DP:AD 0/1:0.047619:42:40,2
#CSQ=T|intergenic_variant|MODIFIER|||||||||||||||rs749868180||||||||T:0.0130|T:0.0047|T:0.0265|T:0.0000|T:0.0083|T:0.0000|||| GT:VF:DP:AD 0/1:1.000000:37:0,37
#CSQ=C|intron_variant|MODIFIER|PTEN|ENSG00000171862|Transcript|ENST00000371953|protein_coding||5/8|ENST00000371953.3:c.492+14T>C|||||||COSM14247||1|HGNC|9588|||||||||||1|1| GT:VF:DP:AD 0/1:0.010707:2802:2772,30
IDs = vep[17].split("&")
dbSNP = ""
cosmic = ""
for ID in IDs:
if ID.startswith("rs"):
if dbSNP == "":
dbSNP = ID
else:
dbSNP += ",%s" % ID
elif ID.startswith("COSM"):
if cosmic == "":
cosmic = ID
else:
cosmic += ",%s" % cosmic
#construct output
output = [
vep[3], vep[8], record[0], record[1], record[3], record[4],
vep[2], type, record[5], altFreq, readDepth, altDepth, vep[1],
vep[22], vep[23], vep[10], vep[11], dbSNP, vep[34]
]
outfile.write("\t".join(output))
outfile.write("\n")
infile.close()
outfile.close()
def parseIlluminaNextseq(infile, outfile):
infile = open(infile, 'r')
outfile = open(outfile, 'w')
for line in infile:
if not line.startswith("#"):
record = line.split("\t")
if len(record[3]) == len(record[4]):
type = "snv"
else:
type = "indel"
vcf = commonTool.vcf(record)
readDepth = vcf.parseInfo("DP")
altFreq = str(float(vcf.parseDetail("VF", 10)) * 100)
alleleDepth = vcf.parseDetail("AD", 10)
altDepth = alleleDepth.split(
",")[1].rstrip() #removes the newline character
vep = vcf.parseInfo("CSQ").split('|')
IDs = vep[17].split("&")
dbSNP = ""
cosmic = ""
for ID in IDs:
if ID.startswith("rs"):
if dbSNP == "":
dbSNP = ID
else:
dbSNP += ",%s" % ID
elif ID.startswith("COSM"):
if cosmic == "":
cosmic = ID
else:
cosmic += ",%s" % ID
#construct output
output = [
vep[3], vep[8], record[0], record[1], record[3], record[4],
vep[2], type, record[5], altFreq, readDepth, altDepth, vep[1],
vep[23], vep[24], vep[10], vep[11], dbSNP, vep[35]
]
outfile.write("\t".join(output))
outfile.write("\n")
infile.close()
outfile.close()
def parseIonNewVarView(infile, outfile):
infile = open(infile, 'r')
outfile = open(outfile, 'w')
for line in infile:
if not line.startswith("#"):
record = line.split("\t")
if len(record[3]) == len(record[4]):
type = "snv"
else:
type = "indel"
vcf = commonTool.vcf(record)
readDepth = vcf.parseInfo("FDP")
altFreq = str(float(vcf.parseInfo("AF")) * 100)
altDepth = vcf.parseInfo("FAO")
vep = vcf.parseInfo("CSQ").split('|')
#parse dbsnp and cosmic from vep field
IDs = vep[17].split("&")
dbSNP = ""
cosmic = ""
for ID in IDs:
if ID.startswith("rs"):
if dbSNP == "":
dbSNP = ID
else:
dbSNP += ",%s" % ID
elif ID.startswith("COSM"):
if cosmic == "":
cosmic = ID
else:
cosmic += ",%s" % ID
globalMinorAllele = ""
globalMinorAleleFreq = ""
alleleFreqAmr = ""
alleleFreqAsn = ""
alleleFreqAfr = ""
alleleFreqEur = ""
try:
globalMinorAllele = vep[25].split(":")[0]
globalMinorAleleFreq = str(float(vep[25].split(":")[1]) * 100)
alleleFreqAmr = str(
float(vep[27].split("&")[0].split(":")[1]) * 100)
alleleFreqAsn = str(
float(vep[28].split("&")[0].split(":")[1]) * 100)
alleleFreqAfr = str(
float(vep[26].split("&")[0].split(":")[1]) * 100)
alleleFreqEur = str(
float(vep[29].split("&")[0].split(":")[1]) * 100)
except IndexError:
pass
#construct output
output = [
vep[3], vep[8], record[0], record[1], record[3], record[4],
vep[2], type, record[5], altFreq, readDepth, altDepth, vep[1],
vep[23], vep[24], vep[10], vep[11], dbSNP, vep[35]
]
outfile.write("\t".join(output))
outfile.write("\n")
infile.close()
outfile.close()