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#!/usr/bin/python
#(c) 2013-2015 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)
"""
This script converts synteny blocks file from Ragout internal format
to one that MLGO recognizes
"""
from __future__ import print_function
from __future__ import absolute_import
import sys
from collections import defaultdict
def main():
if len(sys.argv) != 2:
print("Usage: 2geneorder.py genome_permutations")
return 1
filename = sys.argv[1]
blocks = defaultdict(list)
with open(filename, "r") as f:
while True:
name_str = f.readline().strip()
if not name_str:
break
blocks_str = f.readline().strip()
blocks[name_str[1:].split(".")[0]].append(blocks_str)
for genome, seqs in blocks.items():
print(">{0}".format(genome))
for seq in seqs:
print(seq)
return 0
if __name__ == "__main__":
main()
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