Revision fa6f861d2b8e19b51b98ae6f14782e9b5b6bd6f5 authored by Mikhail Kolmogorov on 28 September 2015, 23:31:21 UTC, committed by Mikhail Kolmogorov on 28 September 2015, 23:31:21 UTC
chromosome-report.py
#!/usr/bin/env python2.7
#(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)
"""
A diagnostic script for chromosome fusions
"""
from __future__ import print_function
import sys
from collections import defaultdict
REF_NAME = "C57B6J"
def do_job(links_file, target_perms, all_blocks):
block_chrs = {}
with open(all_blocks, "r") as f:
for line in f:
line = line.strip()
if line.startswith(">"):
tokens = line[1:].split(".", 1)
genome_name, chr_name = tokens
elif genome_name != REF_NAME:
continue
else:
blocks_ids = map(int, line.split(" ")[:-1])
for b in blocks_ids:
block_chrs[abs(b)] = chr_name
target_chrs = defaultdict(list)
with open(target_perms, "r") as f:
for line in f:
line = line.strip()
if line.startswith(">"):
seq_name = line[1:]
else:
blocks_ids = map(int, line.split(" ")[:-1])
for b in blocks_ids:
block_chr = block_chrs.get(abs(b), None)
if (not block_chr or not target_chrs[seq_name] or
target_chrs[seq_name][-1] != block_chr):
target_chrs[seq_name].append(str(b) + ":" + block_chr)
with open(links_file, "r") as f:
for line in f:
line = line.strip()
if not line or line.startswith("--") or line.startswith("sequence"):
continue
if line[0] not in "+-":
print("\n" + line + "\n")
continue
sign, contig_name = line[0], line.split()[0][1:]
blocks = (target_chrs[contig_name] if sign == "+"
else target_chrs[contig_name][::-1])
print(sign, contig_name, blocks)
def main():
if len(sys.argv) != 4:
print("Usage: chromosome-report.py links target_perms all_perms")
return 1
do_job(sys.argv[1], sys.argv[2], sys.argv[3])
return 0
if __name__ == "__main__":
main()
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