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#!/usr/bin/python3
"""
Read a maf file from stdin and write out a new maf with only blocks having all
of the required in species, after dropping any other species and removing
columns containing only gaps.
usage: %prog species,species2,... < maf
"""
import sys
import bx.align.maf
def main():
species = sys.argv[1].split(",")
maf_reader = bx.align.maf.Reader(sys.stdin, parse_e_rows=True)
maf_writer = bx.align.maf.Writer(sys.stdout)
for m in maf_reader:
new_components = []
for comp in m.components:
if comp.src.split(".")[0] in species:
new_components.append(comp)
m.components = new_components
m.remove_all_gap_columns()
if len(m.components) > 1:
maf_writer.write(m)
maf_reader.close()
maf_writer.close()
if __name__ == "__main__":
main()
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