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#!/usr/bin/python3
"""
Reads a list of intervals and a set of indexed mafs. For each interval print
the amount covered by each species other than the reference.
usage: %prog maf_files [options] < interval_file
-s, --src=s: Use this src for all intervals
-p, --prefix=p: Prepend this to each src before lookup
"""
import sys
from collections import defaultdict
import bx.align.maf
from bx.cookbook import doc_optparse
def __main__():
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
try:
maf_files = args
if options.prefix:
prefix = options.prefix
else:
prefix = None
except Exception:
doc_optparse.exit()
# Open indexed access to mafs
indexes = [bx.align.maf.Indexed(maf_file, maf_file + ".index") for maf_file in maf_files]
# Iterate over input ranges
for line in sys.stdin:
fields = line.split()
src, start, end = fields[0], int(fields[1]), int(fields[2])
if prefix:
src = prefix + src
total_length = end - start
# Find overlap with reference component
blocks = []
for index in indexes:
blocks += index.get(src, start, end)
coverage = defaultdict(int)
for block in blocks:
overlap_start = max(start, block.components[0].start)
overlap_end = min(end, block.components[0].end)
length = overlap_end - overlap_start
assert length > 0
for c in block.components[1:]:
species = c.src.split(".")[0]
coverage[species] += length
print(line, end=" ")
for key, value in coverage.items():
print(" ", key.ljust(10), "%0.2f" % (value / total_length))
if __name__ == "__main__":
__main__()
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