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#!/usr/bin/python3
"""
Read a MAF from stdin and break into several mafs based on the source of
each block. If the `component` option is provided then only that component
will be used to determine the new file for each block, otherwise the src
for *all* components will be used.
TODO: Should be able to specify component by species/prefix?
usage: %prog [options] < maf
-o, --outprefix: prepend this to the name of each generate maf
-c, --component: use only this component (by index!) to split
"""
import string
import sys
from optparse import OptionParser
import bx.align.maf
INF = "inf"
def __main__():
# Parse command line arguments
parser = OptionParser()
parser.add_option("-o", "--outprefix", action="store", default="")
parser.add_option("-c", "--component", action="store", default=None)
(options, args) = parser.parse_args()
out_prefix = options.outprefix
comp = options.component
if comp is not None:
comp = int(comp)
maf_reader = bx.align.maf.Reader(sys.stdin)
writers = {}
for m in maf_reader:
if comp is None:
writer_key = string.join([c.src for c in m.components], "_")
else:
writer_key = m.components[comp].src
if writer_key not in writers:
writer = bx.align.maf.Writer(open(f"{out_prefix}{writer_key}.maf", "w"))
writers[writer_key] = writer
else:
writer = writers[writer_key]
writer.write(m)
for key in writers:
writers[key].close()
if __name__ == "__main__":
__main__()
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