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#!/usr/bin/python3
"""
Read scores in "wiggle" format from `score_file` and intervals in "bed" format
from `interval_file` and print all scores overlapping intervals.
TODO: Support binned array format scores also.
usage: %prog score_file interval_file [out_file]
"""
import sys
import bx.wiggle
from bx import misc
from bx.binned_array import BinnedArray
from bx.cookbook import doc_optparse
def read_scores(f):
scores_by_chrom = {}
for chrom, pos, val in bx.wiggle.Reader(f):
if chrom not in scores_by_chrom:
scores_by_chrom[chrom] = BinnedArray()
scores_by_chrom[chrom][pos] = val
return scores_by_chrom
def main():
# Parse command line
options, args = doc_optparse.parse(__doc__)
try:
score_file = open(args[0])
interval_file = open(args[1])
if len(args) > 2:
out_file = open(args[2], "w")
else:
out_file = sys.stdout
except Exception:
doc_optparse.exit()
scores_by_chrom = read_scores(misc.open_compressed(sys.argv[1]))
for line in open(sys.argv[2]):
fields = line.split()
chrom, start, stop = fields[0], int(fields[1]), int(fields[2])
if chrom in scores_by_chrom:
ba = scores_by_chrom[chrom]
scores = [ba[i] for i in range(start, stop)]
else:
scores = []
print(" ".join(fields), " ".join(map(str, scores)), file=out_file)
score_file.close()
interval_file.close()
out_file.close()
if __name__ == "__main__":
main()
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