Hi everyone,

I am using bx-python to read a bigwig file. However, the current implementation is very slow. A single query in my benchmarks takes about 0.02 seconds in a 2.5Ghz server and I need to run thousands of queries. Through parallelization and other tricks I can read the bigwig faster but I wonder whether anyone knows other library or means to query a bigwig file using python? The perl library to read bigwig files is very fast but I will prefer a python solution.

Update to clarify the problem:

"""
usage: %prog bigwig_file.bw  < bed_file.bed 
"""
from bx.intervals.io import GenomicIntervalReader
from bx.bbi.bigwig_file import BigWigFile
import numpy as np
import time
import sys

bw = BigWigFile( open( sys.argv[1] ) )
ll = []
for interval in GenomicIntervalReader( sys.stdin ):
    start = time.time()
    bw.query(interval.chrom, interval.start, interval.end, 20 ) 
    total = time.time() - start
    ll.append(total)

print np.mean(ll)

This python script will print the average time of each call. For a bed file containing thousands of lines this code may take half an hour while a Perl counterpart using the Bio-BigFile library takes only few seconds.