def sqlComparator( self, sqlrow, out_splt ) :
(chrom1,pos1,ref1,mut1) = sqlrow[1], sqlrow[2],sqlrow[3],sqlrow[4]
coord = out_splt[ self.indexOf["coordinates"] ].split(',')
(chrom2,pos2,strand,refmut) = coord
(ref2,mut2) = refmut.split('/')
return globes.compareVariants( chrom1,pos1,ref1,mut1,\
chrom2,pos2,ref2,mut2 )
def varListSNPComparator(self,variant,out_splt) :
(chrom1,pos1,ref1,mut1) = variant.getPosition()
keys = ['chrom','position','reference','change']
(chrom2,pos2,ref2,mut2) = [ out_splt[ self.indexOf[k] ] for k in keys ]
#print chrom1, pos1, ref1, mut1, chrom2, pos2, ref2, mut2
return globes.compareVariants( chrom1,pos1,ref1,mut1,\
chrom2,pos2,ref2,mut2 )
def varListINDELComparator( self, variant, out_splt ) :
#print 'comparing: %s to %s' % (variant.getPosition(), out_splt )
(chrom1,pos1,ref1,mut1) = variant.getPosition()
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 == 'SNP' : return 1 #want to pass over
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 )
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 comparator(a,b) :
return globes.compareVariants( a[0],a[1],a[2],a[3],b[0],b[1],b[2],b[3] )
def sqlComparator( self, sqlrow, out_splt ) :
(chrom1,pos1,ref1,mut1) = sqlrow[1], sqlrow[2],sqlrow[3],sqlrow[4]
keys = ['chrom','position','reference','change']
(chrom2,pos2,ref2,mut2) = [ out_splt[ self.indexOf[k] ] for k in keys ]
return globes.compareVariants( chrom1,pos1,ref1,mut1,\
chrom2,pos2,ref2,mut2 )
