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#!/usr/bin/python3
"""
For each block in a maf file (read from stdin) write a sequence of ints
corresponding to the columns of the block after applying the provided sequence
mapping.
The 'correct' number of species is determined by the mapping file, blocks not having
this number of species will be ignored.
usage: %prog mapping_file
"""
import sys
import bx.align.maf
from bx import seqmapping
def main():
if len(sys.argv) > 1:
_, alpha_map = seqmapping.alignment_mapping_from_file(open(sys.argv[1]))
else:
alpha_map = None
for maf in bx.align.maf.Reader(sys.stdin):
# Translate alignment to ints
int_seq = seqmapping.DNA.translate_list([c.text for c in maf.components])
# Apply mapping
if alpha_map:
int_seq = alpha_map.translate(int_seq)
# Write ints separated by spaces
for i in int_seq:
print(i, end=" ")
print()
if __name__ == "__main__":
main()
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