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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 checks correctness of Ragout results
if a 'true' reference is available
"""
from __future__ import print_function
from __future__ import absolute_import
import sys
import os
import argparse
from collections import namedtuple
from itertools import product
from utils.nucmer_parser import parse_nucmer_coords
from utils.common import (filter_by_coverage, join_collinear,
group_by_chr, get_order)
from six.moves import map
Scaffold = namedtuple("Scaffold", ["name", "contigs"])
Contig = namedtuple("Contig", ["name", "sign"])
def parse_links_file(filename):
scaffolds = []
def add_contig(string):
name = string.replace("=", "_") #fix for nucmer
without_sign = name[1:].strip()
if "[" in without_sign:
without_sign = without_sign[:without_sign.index("[")]
sign = 1 if name[0] == "+" else -1
scaffolds[-1].contigs.append(Contig(without_sign, sign))
with open(filename, "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 ["+", "-"]:
scaffolds.append(Scaffold(line, []))
else:
left_cont = line.split()[0]
add_contig(left_cont)
#add_contig(right_cont)
return scaffolds
def parse_ord_file(filename):
scaffolds = []
with open(filename, "r") as f:
for line in f:
line = line.strip()
if not line:
continue
if line.startswith(">"):
scaffolds.append(Scaffold(line[1:], []))
else:
sign = 1 if line[0] == "+" else -1
scaffolds[-1].contigs.append(Contig(line[1:], sign))
return scaffolds
def parse_contigs_order(filename):
_filename, ext = os.path.splitext(filename)
if ext[1:] == "ord":
return parse_ord_file(filename)
else:
return parse_links_file(filename)
def gap_count(lst_1, lst_2):
if not lst_1 or not lst_2:
return 0
gaps = sys.maxsize
for i, j in product(lst_1, lst_2):
gaps = min(gaps, abs(i.index - j.index) - 1)
return gaps
def agreement_ord(increasing, lst_1, lst_2, chr_len_dict):
if not lst_1 or not lst_2:
return True
for i, j in product(lst_1, lst_2):
same_chr = i.chr == j.chr
if not same_chr:
continue
chr_len = chr_len_dict[i.chr]
lower = chr_len * 0.2
higher = chr_len * 0.8
over_zero = ((increasing and i.coord > higher and j.coord < lower) or
(not increasing and i.coord < lower and j.coord > higher))
if ((j.index > i.index) == increasing and
abs(i.coord - j.coord) < chr_len / 1) or over_zero:
return True
return False
def agreement_strands(lst_1, lst_2, increasing):
incr_sign = 1 if increasing else -1
for i, j in product(lst_1, lst_2):
if i == j and i == incr_sign:
return True
return False
def do_job(nucmer_coords, scaffolds_ord):
alignment = parse_nucmer_coords(nucmer_coords)
alignment = join_collinear(alignment)
alignment = filter_by_coverage(alignment, 0.45)
entry_ord, chr_len, contig_len = get_order(alignment)
scaffolds = parse_contigs_order(scaffolds_ord)
total_breaks = 0
total_gaps = 0
total_contigs = 0
for s in scaffolds:
print("\n>" + s.name)
prev_aln = []
prev_strand = None
increasing = None
breaks = []
for contig in s.contigs:
miss_ord = False
miss_strand = False
#checking order
if prev_aln:
if increasing is not None:
if not agreement_ord(increasing, prev_aln,
entry_ord[contig.name], chr_len):
increasing = None
breaks.append(contig.name)
total_breaks += 1
miss_ord = True
elif len(entry_ord[contig.name]) == 1 and len(prev_aln) == 1:
increasing = (entry_ord[contig.name][0].index >
prev_aln[0].index)
#checking strand
cur_strand = [h.sign * contig.sign for h in entry_ord[contig.name]]
if not miss_ord and prev_strand and cur_strand:
if not agreement_strands(prev_strand, cur_strand, increasing):
breaks.append(contig.name)
total_breaks += 1
miss_strand = True
increasing = None
if gap_count(prev_aln, entry_ord[contig.name]) > 0:
total_gaps += 1
#only if this contig has alignments
if entry_ord[contig.name]:
prev_aln = entry_ord[contig.name]
prev_strand = cur_strand
#output
sign = "+" if contig.sign > 0 else "-"
pos_list = list(map(str, entry_ord[contig.name]))
pos_list_str = (str(pos_list) if len(pos_list) < 5 else
str(pos_list[:5]) + "...")
print("{0}{1}\t{2}\t{3}".format(sign, contig.name,
contig_len[contig.name], pos_list_str),
end="")
print("\t<<<order" if miss_ord else "", end="")
print("\t<<<strand" if miss_strand else "", end="")
print("")
total_contigs += 1
###
print("\tmiss-ordered: ", len(breaks))
print("\nTotal miss-ordered:", total_breaks)
print("Total gaps:", total_gaps)
print("Total contigs:", total_contigs)
print("Total scaffolds:", len(scaffolds))
def main():
descr = ("A verification script for Ragout. It requires a contigs "
"alignment on \"true\" reference in nucmer coords format. "
"Given an alignment and a \"links\" file output by Ragout "
"the script finds missassembled contigs and calculates some "
"statistics.")
parser = argparse.ArgumentParser(description=descr)
parser.add_argument("nucmer_coords", metavar="nucmer_coords",
help="path to contigs alignment on 'true' reference")
parser.add_argument("links_file", metavar="links_file",
help="path to 'links' file output by Ragout")
args = parser.parse_args()
do_job(args.nucmer_coords, args.links_file)
if __name__ == "__main__":
main()
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