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#!/usr/bin/python3
"""
Create a bed file listing all the divergent sites between two specific species
in a maf.
usage: %prog maf_file reference_species_name other_species_name
"""
import sys
import bx.align.maf
import bx.bitset
def main():
bitsets = {}
maf = sys.argv[1]
reference_sp, other_sp = sys.argv[2], sys.argv[3]
for block in bx.align.maf.Reader(open(maf)):
ref = block.get_component_by_src_start(reference_sp)
other = block.get_component_by_src_start(other_sp)
if not ref or not other:
continue
ref_chrom = ref.src.split(".")[1]
ref_start = ref.start
chrom_size = ref.get_src_size()
if ref_chrom not in bitsets:
bitsets[ref_chrom] = bx.bitset.BinnedBitSet(chrom_size)
pos = ref_start
for i, j in zip(ref.text.upper(), other.text.upper()):
if i != "-":
if i != j: # mismatch
if i != "N" and j != "N" and j != "-":
# set if all valid chars
bitsets[ref_chrom].set(pos)
pos += 1
# bits --> bed file
for chrom in bitsets:
bits = bitsets[chrom]
end = 0
while True:
start = bits.next_set(end)
if start == bits.size:
break
end = bits.next_clear(start)
print("%s\t%d\t%d" % (chrom, start, end))
main()
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