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#!/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)
"""
This script counts number of rearrangements between two assemblies
thus evaluating 'agreement level' between them
"""
from __future__ import print_function
from __future__ import absolute_import
from collections import defaultdict
import sys
import os
import argparse
import networkx as nx
from utils.lastz_parser import (parse_lastz_maf, run_lastz,
filter_intersecting, filter_by_length)
from six.moves import map
from six.moves import zip
def get_alignment(reference, target, overwrite):
out_file = (os.path.basename(reference) + "_" +
os.path.basename(target) + ".maf")
if os.path.isfile(out_file) and not overwrite:
print("Alignment file already exists, lastz run skipped")
else:
run_lastz(reference, target, out_file)
alignment = parse_lastz_maf(out_file)
return alignment
def get_blocks(reference, target, overwrite, min_alignmtnt):
alignment = get_alignment(reference, target, overwrite)
alignment = filter_by_length(alignment, min_alignmtnt)
alignment = filter_intersecting(alignment)
#alignment = join_collinear(alignment)
def enum_blocks(aln_rows):
blocks = defaultdict(list)
for r_id, row in enumerate(aln_rows):
blocks[row.seq_id].append((r_id, row))
for seq_id in blocks:
blocks[seq_id].sort(key=lambda pair: pair[1].start)
to_block = lambda r_id_row: (r_id_row[0] + 1) * r_id_row[1].strand
blocks[seq_id] = list(map(to_block, blocks[seq_id]))
return blocks
#IMPORTANT: ref/qry rows should have corresponding order
ref_blocks = enum_blocks([ap.ref for ap in alignment])
qry_blocks = enum_blocks([ap.qry for ap in alignment])
return ref_blocks, qry_blocks
def output_blocks(blocks):
for seq, bl in blocks.items():
print(">{0}".format(seq))
print(" ".join(["{0:+d}".format(b) for b in bl]))
def count_discord_adj(ref_blocks, qry_blocks):
#building breakpoint graph
graph = nx.MultiGraph()
for seq, blocks in ref_blocks.items():
for block_1, block_2 in zip(blocks[:-1], blocks[1:]):
graph.add_edge(-block_1, block_2, name=seq, color="blue")
for seq, blocks in qry_blocks.items():
for block_1, block_2 in zip(blocks[:-1], blocks[1:]):
graph.add_edge(-block_1, block_2, name=seq, color="green")
counter = 0
for node in graph.nodes:
if len(graph.neighbors(node)) > 1:
counter += 1
return counter
def main():
parser = argparse.ArgumentParser(description="Compare two assemblies")
parser.add_argument("assembly_1", metavar="assembly_1",
help="path to first assembly")
parser.add_argument("assembly_2", metavar="assembly_2",
help="path to second assembly")
parser.add_argument("--overwrite", action="store_const", metavar="overwrite",
dest="overwrite", default=False, const=True,
help="overwrite existing lastz alignment")
parser.add_argument("-b", "--block", dest="block_size",
help="minimum synteny block size",
default="5000")
args = parser.parse_args()
ref_blocks, qry_blocks = get_blocks(args.assembly_1, args.assembly_2,
args.overwrite, int(args.block_size))
#output_blocks(ref_blocks)
#output_blocks(qry_blocks)
print(count_discord_adj(ref_blocks, qry_blocks))
if __name__ == "__main__":
main()
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