bx-python / scripts / bed_bigwig_profile.py

#!/usr/bin/env python

Create a site profile vector showing the average signal accumulated from a
bigwig file around the center of each interval from a BED file.

Output is the average signal value at that relative position across the 

usage: %prog bigwig_file.bw padding < bed_file.bed 

import sys
from numpy import *

from bx.intervals.io import GenomicIntervalReader
from bx.bbi.bigwig_file import BigWigFile

bw = BigWigFile( open( sys.argv[1] ) )
padding = int( sys.argv[2] )
totals = zeros( padding*2, dtype=float64 )
valid = zeros( padding*2, dtype=int32 )

for interval in GenomicIntervalReader( sys.stdin ):
    center = floor( ( interval.start + interval.end ) / 2 )
    values = bw.get_as_array( interval.chrom, center - padding, center + padding )
    # Determine which positions had data and mask the rest for totalling
    invalid = isnan( values )
    values[ invalid ] = 0
    totals += values
    valid += ( ~ invalid )

savetxt( sys.stdout, totals/valid )
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