class VcfFile(object):
'a class representing a VCF file'
def __init__(self, filename):
self.metaline = MetaLines()
self.headerline = HeaderLines()
self.miscline = MiscLines()
self.filename=filename
def parseMetaAndHeaderLines(self, fh):
""" parse meta lines that begin with ## and header line that begins with # """
for line in fh:
if '##fileformat' in line.strip():
self.metaline.setFileFormat(line.strip())
elif '##INFO' in line.strip():
self.metaline.parseMetaInfo(line)
elif '##FILTER' in line.strip():
self.metaline.parseMetaFilter(line)
elif '##FORMAT' in line.strip():
self.metaline.parseMetaFormat(line)
elif '#CHROM' in line.strip():
self.headerline.add_format_column(line.strip() )
self.headerline.append_samplelist( line.strip() )
break
else:
self.miscline.parseMiscInfo(line)
def parseMetaLines(self, fh):
""" parse the meta lines that begin with ## in a VCF file """
for line in fh:
#print "foo "+ line.strip()
if '##fileformat' in line.strip():
self.metaline.setFileFormat(line)
elif '##INFO' in line.strip():
self.metaline.parseMetaInfo(line)
elif '##FILTER' in line.strip():
self.metaline.parseMetaFilter(line)
elif '##FORMAT' in line.strip():
self.metaline.parseMetaFormat(line)
elif '#CHROM' in line.strip():
self.headerline.add_format_column(line.strip() )
self.headerline.append_samplelist( line.strip() )
self.printHeaderLine()
break
#elif '##reference' in line.strip():
#break
else:
self.miscline.parseMiscInfo( line.strip() )
def hasFormatHeader(self,headerline):
""" check if header line has FORMAT column """
self.headerline.add_format_column(headerline)
def parseHeaderLine(self,fh):
for line in fh:
#print line.strip()
if '#CHROM' not in line:
break
self.headerline.add_format_column(line.strip() )
self.headerline.append_samplelist( line.strip() )
break
def printHeaderLine(self):
print self.headerline.toString()
def getSampleList(self):
return self.headerline.getSampleList()
def setSampleList(self, newlist):
self.headerline.setSampleList(newlist)
def getMetaInfoNames(self):
""" return the IDs of the INFO metalines"""
return self.metaline.getMetaInfoNames()
def getMetaInfoDescription(self):
return self.metaline.getMetaInfoDescription()
def addMetaInfoHeader(self, id, type, number, description):
""" add an ##INFO header to a vcf file """
self.metaline.addMetaInfo(id, type,number,description)
def addMetaFilterHeader(self, id, description):
""" add ##FILTER header to a vcf file """
self.metaline.addMetaFilter(id, description)
def getMetaFilterNames(self):
""" return the IDs of the FILTER metalines """
return self.metaline.getMetaFilterNames()
def getMetaFilterDescription(self):
""" return a list of tuples with (id, description) of FILTER metalines """
return self.metaline.getMetaFilterDescription()
def getMetaFormatNames(self):
""" return the Ids of the FORMAT metalines"""
return self.metaline.getMetaFormatNames()
def addMetaFormatHeader(self, formatObj):
""" add a ##FORMAT header """
self.metaline.addMetaFormat(formatObj)
def getMetaFormatDescription(self):
""" return a list of tuples (id,descripton) for FORMAt metalines """
return self.metaline.getMetaFormatDescription()
def yieldMetaInfoLines(self):
""" yield string representation of ##INFO metalines """
return self.metaline.yieldPrintMetaInfoLines()
def yieldMetaFormatLines(self):
""" yield string reprsentation ##FORMAT metaline object """
return self.metaline.yieldPrintMetaFormatLines()
def yieldMetaFilterLines(self):
""" yield string represenation of ##FILTER metaline object """
return self.metaline.yieldPrintMetaFilterLines()
def printMetaInfoLines(self):
"""print the meta ##INFO lines for a VCF """
for str in self.yieldMetaInfoLines():
print str
def printMetaFormatLines(self):
for str in self.yieldMetaFormatLines():
print str
def printMetaFilterLines(self):
for str in self.yieldMetaFilterLines():
print str
def printMetaLines(self):
self.printMetaInfoLines()
self.printMetaFormatLines()
self.printMetaFilterLines()
""" collect all the lines that start with ## and #CHROM and rturn a string """
def returnHeader(self):
headerlines=[]
fileformat=self.metaline.getFileFormat()
headerlines.append(fileformat)
for str in self.yieldMetaInfoLines():
headerlines.append(str)
for str in self.metaline.yieldPrintMetaFormatLines():
headerlines.append(str)
for str in self.yieldMetaFilterLines():
headerlines.append(str)
for str in self.miscline.yieldPrintMiscInfo():
headerlines.append(str)
headerlines.append( self.headerline.toString() )
outstr="\n".join(headerlines)
return outstr
def printMetaAndHeaderLines(self):
print self.returnHeader()
def yieldVcfRecord(self,fh):
""" yield VcfRecord object from reading a dataline in a VCF file """
for line in fh:
#print line.strip()
if '#' in line: continue
fields=line.strip().split('\t')
(chrom,pos,id,ref,alt,qual,filter,info)=fields[0:8]
yield VcfRecord(chrom,pos,id,ref,alt,qual,filter,info)
def yieldVcfDataLine(self,fh):
""" yield dataline from filehandle fh reprsenting a vcf file """
for line in fh:
if '#' in line:continue
yield line.strip()
def yieldVcfRecordwithGenotypes(self,fh):
""" yield a VcfRecord with its genotypes list populated """
for line in fh:
fields=line.strip().split('\t')
(chrom,pos,id,ref,alt,qual,filter,info)=fields[0:8]
vrec=VcfRecord(chrom,pos,id,ref,alt,qual,filter,info)
formatstring=fields[8]
(genotypestrings)=fields[9::]
for gstring in genotypestrings:
vrec.addGenotype( VcfGenotype(formatstring,gstring))
yield vrec
def printDataLineWithGenotypes(self,vcfh):
for vrec in self.yieldVcfRecordwithGenotypes(vcfh):
print vrec.toStringwithGenotypes()
def __init__(self, filename):
self.metaline = MetaLines()
self.headerline = HeaderLines()
self.miscline = MiscLines()
self.filename=filename
