def integrator(self, target, splts) :
#this is a one to many match with SeattleSeq
assert len(splts) == 1
splt = splts[0]
#transition from variant fields to JointCall fields
ix = 4
splt[0] = chromNum( splt[0] )
fields = dict( zip( headers[:ix], splt[:ix] ) )
jc = JointCall( self.pat_name )
jc.fields = dict( zip( headers[ix:], splt[ix:] ) )
jc.fields["GT"] = convertGT( splt[-9:] )
return Variant( fields, [jc] )
def integrator( self, target, splts ) :
if len(splts) != 1 : assert "len isn't right"
for splt in splts :
calls = splt[ CALL_START: ]
base_calls = []
for pat_ix,c in enumerate(calls) :
pat_name = self.patients[pat_ix]
sc = splitCall(c)
gt = convertGT( sc )
if isMutated( gt ) or noInf( gt ) :
base_calls.append( variant.BaseCall(sc,pat_name) )
fields = {}
keys = COLUMN_MAP.keys()
for k in keys :
if k == "chrom" :
fields[k] = globes.chromNum( splt[self.indexOf[k]] )
elif k == "info" :
#this information is useless, will get globally updated
dinfo = makeInfoDict( splt[ self.indexOf[k] ] )
fields["AF"] = dinfo["AF"]
elif k == "dbSNP" :
value = splt[self.indexOf[k]]
#when we getFields, 'dbsnp' will be missing and yield null
if value == '.' : pass
#right now just take the first rs number if multiple
elif value.startswith('rs') :
fields[k] = [int(t.strip()[2:]) for t in value.split(';')][0]
else :
print "malformed rs number?", splt
assert False
else :
fields[k] = splt[ self.indexOf[k] ]
#according to: http://www.broadinstitute.org/gsa/wiki/index.php/Understanding_the_Unified_Genotyper's_VCF_files
#ref and alt are always given for the forward strand
fields['strand'] = True
#TODO
#This is abusing that fact that VCFSource goes first in the collimator
#o/w will overwrite what has been put in target
return variant.Variant( fields, base_calls )
def integrator( self, target, splts ) :
if len(splts) != 1 : assert "len isn't right"
for splt in splts :
##TODO generalize this to make it vendor independent, call start column is feature of VCF, not broad???
calls = splt[ broad.CALL_START: ]
base_calls = []
for pat_ix,c in enumerate(calls) :
sc = broad.splitCall(c)
gt = broad.convertGT( sc )
if broad.isMutated( gt ) or broad.noInf( gt ) :
base_calls.append( BaseCall(sc,pat_ix) )
fields = {}
keys = broad.COLUMN_MAP.keys()
for k in keys :
if k == "chrom" :
fields[k] = globes.chromNum( splt[self.indexOf[k]] )
elif k == "info" :
##TODO generalize this to make it vendor independent
dinfo = broad.makeInfoDict( splt[ self.indexOf[k] ] )
fields["AF"] = dinfo["AF"]
elif k == "dbSNP" :
value = splt[self.indexOf[k]]
#when we getFields, 'dbsnp' will be missing and yield null
if value == '.' : pass
#right now just take the first rs number if multiple
elif value.startswith('rs') :
fields[k] = [int(t.strip()[2:]) for t in value.split(';')][0]
else :
print "malformed rs number?", splt
assert False
else :
fields[k] = splt[ self.indexOf[k] ]
#according to: http://www.broadinstitute.org/gsa/wiki/index.php/Understanding_the_Unified_Genotyper's_VCF_files
#ref and alt are always given for the forward strand
fields['strand'] = True
return Variant( fields, base_calls )
def eqkey( self, out_splt ) :
if self.switch == 'snp' :
keys = ['chrom','position','reference','change']
(chrom,pos,ref,mut) = [ out_splt[ self.indexOf[k] ] for k in keys ]
return (globes.chromNum(chrom),pos,ref,mut)
elif sel.switch == 'indel' :
keys = ['chrom','position','reference','change', "change type"]
(chrom2,pos2,ref2,mut2,change_type) = \
[ out_splt[ self.indexOf[k] ] for k in keys ]
if change_type == 'INS' :
#example:
# 1 866511 rs60722469 C CCCCT
# 1 866512 * +CCCT INS
return globes.compareVariants( chrom1, pos1, ref1, mut1[1:], \
chrom2, int(pos2)-1, ref2, mut2[1:] )
elif change_type == 'DEL' :
#1 874864 . CT C
#1 874865 * -T DEL Het
return globes.compareVariants( chrom1, pos1, ref1[1:], mut1, \
chrom2, int(pos2)-1, mut2[1:], ref2 )
else :
assert "change_type %s is not" % change_type == " INS or DEL"
else : assert 'switch must be' == ' snp or indel'
def sortHelper( it ) :
return (chromNum(it[0]),int(it[1]))
def getPosition( self, out_splt ) :
if self.switch == 'snp' :
#if it was called with parsed input, there will be only one thing in
#the sampleGenotype column, rather than info for everyone
if False : #len( out_splt[self.indexOf["sampleGenotype"]] ) == 1 :
keys = ["chromosome","position", \
"referenceBase","sampleGenotype"]
(chrom2,pos2,ref2,mut2) = [out_splt[self.indexOf[k]] \
for k in keys]
#otherwise it is easier to use sampleAlleles
else :
keys = ["chromosome","position","referenceBase","sampleAlleles"]
(chrom2,pos2,ref2,als) = [out_splt[self.indexOf[k]] for k in keys]
sp = als.split('/')
#split up the sample alleles, find which one matches the ref
if len(sp) == 2 :
(a1,a2) = sp
if a1 == ref2 : mut2 = a2
elif a2 == ref2 : mut2 = a1
else :
#print out_splt
mut2 = 'N'
#assert "Have a problem" == "with figuring out mut2"
elif len(sp) == 1 :
mut2 = sp[0]
else :
assert "length of sampleAllelels" == "not == 2 or 1"
#what is going on with the *'s, exactly?
elif self.switch == 'indel' :
keys = ['chromosome','position','referenceBase','sampleGenotype']
(chrom2,pos2,ref2,sg) = [out_splt[self.indexOf[k]] for k in keys]
samples = sg.split(',')
mut2 = ""
isInsertion = '-' in ref2
# go through each sample, find the first allele different
# from the ref
# when we can't match, use wildcard '*',
# globes.compareVariants will know how to use
if isInsertion :
ref2 = ref2[0]
for sample in samples :
(one,two) = sample.split('/')
if ref2 != one :
mut2 = one
break
elif ref2 != two :
mut2 = two
break
else : continue
if mut2 == 'N' or mut2 == '' : mut2 = '*'
else :
for sample in samples :
(one,two) = sample.split('/')
if one[1:] == ref2 :
ref2 = one
mut2 = one[0]
break
elif two[1:] == ref2 :
ref2 = two
mut2 = two[0]
break
else : continue
if mut2 == "" :
ref2 = '*'
mut2 = '*'
else : assert 'switch must be' == 'snp or indel'
if mut2 == 'N' : mut2 = '*'
#print 'seattle pos: ',chrom2, pos2, ref2, mut2
return (globes.chromNum(chrom2),pos2,ref2,mut2)
def sortHelper( splt ) :
return (globes.chromNum(splt[1]), int(splt[2]) )
fin = open("../preliminary/%s" % fname)
fout = open("../preliminary/%s.functional.tsv" % patient,'w')
csvout = csv.writer( fout,\
delimiter='\t', \
quoting=csv.QUOTE_MINIMAL )
csvout.writerow( queries.column_headers )
hits = 0
already_called = 0
total = 0
for line in fin.readlines() :
splt = line.split()
chrom, pos = splt[0], splt[1]
#print chrom, pos
chrom = globes.chromNum( chrom )
if not chrom : continue
query = '''
select %s,%s,%s
from Variants as v inner join Isoforms as i on i.var_id = v.id
inner join Genes as g on g.id = i.gene_id
where chrom = %s and pos = %s and AF < .1 and (%s)''' % \
(queries.vcols_string, queries.icols_string, queries.gcols_string, \
chrom, pos, queries.gvs)
rows = conn.query(query)
num_rows = len(rows)
if num_rows > 0 :
hits += 1
def sortHelper( line ) :
[chrom,loc] = line.strip().split('\t')[0].split(',')[0:2]
return ( globes.chromNum(chrom), int(loc) )
def getPosition( self, out_splt ) :
if self.switch == 'snp' :
#if it was called with parsed input, there will be only one thing in
#the sampleGenotype column, rather than info for everyone
if False : #len( out_splt[self.indexOf["sampleGenotype"]] ) == 1 :
keys = ["chromosome","position","referenceBase","sampleGenotype"]
(chrom2,pos2,ref2,mut2) = [out_splt[self.indexOf[k]] for k in keys]
#otherwise it is easier to use sampleAlleles
else :
keys = ["chromosome","position","referenceBase","sampleAlleles"]
(chrom2,pos2,ref2,als) = [out_splt[self.indexOf[k]] for k in keys]
sp = als.split('/')
if len(sp) == 2 :
(a1,a2) = sp
if a1 == ref2 : mut2 = a2
elif a2 == ref2 : mut2 = a1
else : assert "Have a problem" == "with figuring out mut2"
elif len(sp) == 1 :
mut2 = sp[0]
else :
assert "length of sampleAllelels" == "not == 2 or 1"
#what is going on with the *'s, exactly?
elif self.switch == 'indel' :
keys = ['chromosome','position','referenceBase','sampleGenotype']
(chrom2,pos2,ref2,sg) = [out_splt[self.indexOf[k]] for k in keys]
#print "readiung: ", chrom2, pos2, ref2, sg
samples = sg.split(',')
mut2 = ""
isInsertion = '-' in ref2
if isInsertion :
ref2 = ref2[0]
for sample in samples :
(one,two) = sample.split('/')
if ref2 != one :
mut2 = one
break
elif ref2 != two :
mut2 = two
break
else : continue
if mut2 == 'N' or mut2 == '' : mut2 = '*'
else :
for sample in samples :
(one,two) = sample.split('/')
if one[1:] == ref2 :
ref2 = one
mut2 = one[0]
break
elif two[1:] == ref2 :
ref2 = two
mut2 = two[0]
break
else : continue
if mut2 == "" :
ref2 = '*'
mut2 = '*'
else : assert 'switch must be' == 'snp or indel'
#not ideal, but if SeattleSeq is going to be a bitch
#it's the best we can do
if mut2 == 'N' : mut2 = '*'
#print "returning: ", chrom2, pos2, ref2, mut2
return (globes.chromNum(chrom2),pos2,ref2,mut2)
