def pickOutFamilies( orig_filename, outdir,family_groups, \
callToString = lambda x:x,\
lineFilter = lambda x:True, \
cols_to_use = range(len(COLUMN_MAP)), \
) :
fin = open( orig_filename, "rb" )
#open filehandles for each group, initialize group's column index list
if not os.path.isdir(outdir) : os.mkdir(outdir)
fouts = {}
groupIXs = {}
for group in family_groups :
safe_group = sanitizePatientName( group )
fouts[group] = open( "%s/%s.vcf" % (outdir,safe_group), 'wb' )
groupIXs[group] = []
(columns,headers) = getColumnsAndHeaders( fin )
header_string = "\n".join(headers)
for i in range( len(columns) ) :
for group in family_groups :
family_names = family_groups[group]
print columns[i], family_names
if columns[i] in family_names :
groupIXs[group].append( i )
print groupIXs
#print headers
for group in family_groups :
fouts[group].write( "%s\n" % header_string )
out_header = '\t'.join( [columns[i] for i in \
cols_to_use + groupIXs[group]] )
fouts[group].write( "%s\n" % out_header )
#fouts[group].write( '\n'.join(columns) )
#fouts[group].write( "%s\n" % out_header )
# 'indexOf' dictionary maps header string to it's column index
#in the input file
indexOf = COLUMN_MAP
globes.printColumnWarning( orig_filename, indexOf )
# process the data lines
for dataline in fin.readlines() :
splt = dataline.strip().split('\t')
if lineFilter( splt ) :
data = [splt[ix] for ix in cols_to_use]
for group in family_groups :
calls = [ callToString(splt[ix]) for ix in groupIXs[group] ]
string = "%s\t%s\n" % ( '\t'.join(data), '\t'.join(calls))
fouts[group].write( string )
#close filehandles for each group
for group in fouts :
fouts[group].close()
fin.close()
def __init__(self, vcf_file, fast_forward=0) :
self.indexOf = COLUMN_MAP
globes.printColumnWarning( vcf_file, self.indexOf )
self.fin = open( vcf_file, "rb" )
self.patients = getPatients( self.fin )
print "after getPatients"
self.allow_absent = False
self.group_repeats = False
self.iterator = globes.splitIterator( self.fin, burn=fast_forward )
def __init__(self, vcf_file, fast_forward=0) :
self.indexOf = broad.COLUMN_MAP
globes.printColumnWarning( vcf_file, self.indexOf )
self.fin = open( vcf_file, "rb" )
self.patients = broad.getPatients( self.fin )
self.allow_absent = False
self.group_repeats = False
self.iterator = self.iterate(fast_forward)