def bam2graph( bam,contig,window ):
""" """
#first get mean coverage
c2cs = get_contig2coverage( bam )
gsize = sum( [ s for c,s in c2cs.itervalues() ] )
rcount = sum( [ c for c,s in c2cs.itervalues() ] )
expcount = 1.0 * rcount * window / gsize
#generate graph data
gdata = []
clen = c2cs[contig][1]
sam = pysam.Samfile( bam )
for i in xrange( 0,clen,window ):
#log2 = 0
c = sam.count( reference=contig,start=i,end=i+window )
if c:
#last window is shorter!
if i+window>clen:
expcount = 1.0 * rcount * (clen-i) / gsize
log2 = log( c/expcount,2 )
gdata.append( (i+1,log2) )
return gdata,clen
def bam2graph( bam,contig,window ):
""" """
#first get mean coverage
c2cs = get_contig2coverage( bam )
gsize = sum( [ s for c,s in c2cs.itervalues() ] )
rcount = sum( [ c for c,s in c2cs.itervalues() ] )
expcount = 1.0 * rcount * window / gsize
#generate graph data
gdata = []
clen = c2cs[contig][1]
sam = pysam.Samfile( bam )
for i in xrange( 0,clen,window ):
#log2 = 0
c = sam.count( reference=contig,start=i,end=i+window )
if c:
#last window is shorter!
if i+window>clen:
expcount = 1.0 * rcount * (clen-i) / gsize
log2 = log( c/expcount,2 )
gdata.append( (i+1,log2) )
return gdata,clen