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#!/usr/bin/python3
"""
Application to convert LAV file to MAF file. Reads a LAV file from standard
input and writes a MAF file to standard out; some statistics are written to
standard error.
usage: lav_to_maf [--silent] [path=replacement] < lav_file > maf_file
"""
import sys
import bx.align.lav
import bx.align.maf
def usage(s=None):
message = __doc__
if s is None:
sys.exit(message)
else:
sys.exit(f"{s}\n{message}")
def main():
# parse the command line
silent = False
pathSubs = []
for arg in sys.argv[1:]:
if "=" in arg:
ix = arg.find("=")
pathSubs.append((arg[:ix], arg[ix + 1 :]))
elif arg == "--silent":
silent = True
else:
usage("unrecognized argument: " + arg)
# read the alignments and other info
out = bx.align.maf.Writer(sys.stdout)
lavsRead = mafsWritten = 0
for lavBlock in bx.align.lav.Reader(sys.stdin, path_subs=pathSubs):
lavsRead += 1
out.write(lavBlock)
mafsWritten += 1
if not silent:
sys.stderr.write("%d blocks read, %d written\n" % (lavsRead, mafsWritten))
if __name__ == "__main__":
main()
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