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#!/usr/bin/python3
############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# All Rights Reserved
# See file LICENSE for details.
############################################################################
import SeqIO
from SeqIO import SeqRecord
import sys
import os
import shutil
import sam_parser
import itertools
def ConstructCoverage(sam, contigs, k):
cov = dict()
for contig in range(len(contigs)):
cov[contig] = [0] * (len(contigs[contig]) + 1)
reads = []
for rec in sam:
reads.append(rec)
if len(reads) == 2:
if reads[0].proper_alignment:
if reads[0].pos + k - 1 < reads[1].pos + reads[1].alen - k:
cov[reads[0].tid][reads[0].pos + k - 1] += 1
cov[reads[0].tid][reads[1].pos + reads[1].alen - k] -= 1
else:
if reads[1].pos + k - 1 < reads[0].pos + reads[0].alen - k:
cov[reads[1].tid][reads[1].pos + k - 1] += 1
cov[reads[0].tid][reads[0].pos + reads[0].alen - k] -= 1
reads = []
return cov
def ConstructCoverageSingle(sam, contigs, k):
cov = dict()
for contig in range(len(contigs)):
cov[contig] = [0] * (len(contigs[contig]) + 1)
for rec in sam:
if rec.proper_alignment:
if rec.pos + k - 1 < rec.pos + rec.alen - k:
cov[rec.tid][rec.pos + k - 1] += 1
cov[rec.tid][rec.pos + rec.alen - k] -= 1
return cov
def OutputHist(cov, contigs, folder):
if os.path.exists(folder):
shutil.rmtree(folder)
os.makedirs(folder)
for contig in range(len(contigs)):
f = open(folder + "/" + contigs[contig].id, "w")
cur = 0
for i in range(len(cov[contig])):
cur += cov[contig][i]
f.write(str(i) + " " + str(cur) + "\n")
f.close()
def ConstructSimpleCoverage(sam, contigs, k):
simple_cov = dict()
for contig in range(len(contigs)):
simple_cov[contig] = [0] * (len(contigs[contig]) + 1)
for rec in sam:
if not rec.is_unmapped:
simple_cov[rec.tid][rec.pos] += 1
simple_cov[rec.tid][rec.pos + rec.alen] -= 1
return simple_cov
def BreakContig(cov, k, min0):
l = len(cov) - 1
if l < 2 * k:
return []
result = []
cur = 0
cur_len0 = 0
prev_break = 0
for i in range(l):
cur += cov[i]
if cur == 0:
cur_len0 += 1
else:
if cur_len0 == i:
prev_break = max(0, i - k)
elif cur_len0 > min0:
result.append([prev_break, i - cur_len0])
prev_break = i
cur_len0 = 0
result.append([prev_break, min(l, l - cur_len0 + k)])
return result
class ContigBreaker:
def __init__(self, contigs, sam, k, min0):
self.part_list_ = []
self.contigs = contigs
self.sam = sam
cov = ConstructCoverage(self.sam, contigs, k)
# OutputHist(cov, contigs, "tmp")
# simple_cov = ConstructSimpleCoverage(sam, k)
for contig in range(len(contigs)):
parts = BreakContig(cov[contig], k, min0)
self.part_list_.append(parts)
def Break(self, contig):
result = []
#print contig.id
#print self.sam.gettid(contig.id)
for part in self.part_list_[self.sam.gettid(contig.id)]:
result.append(contig.subseq(part[0], part[1]))
return result
def OutputBroken(self, output_file):
output = open(output_file, "w")
for contig in self.contigs:
for subcontig in self.Break(contig):
SeqIO.write(subcontig, output, "fasta")
output.close()
class PatternBreaker:
def __init__(self, pattern, rc_pattern, max_cut):
self.pattern = pattern
self.rc_pattern = rc_pattern
self.max_cut = max_cut
def FindLeftPos(self, seq):
l1 = seq.find(self.pattern)
l2 = seq.find(self.rc_pattern)
if l1 == -1:
l1 = len(seq)
if l2 == -1:
l2 = len(seq)
l = min(l1, l2) + len(self.pattern)
if l < self.max_cut:
return l
else:
return 0
def FindRightPos(self, seq):
l1 = seq.rfind(self.pattern)
l2 = seq.rfind(self.rc_pattern)
if l1 == -1:
l1 = 0
if l2 == -1:
l2 = 0
l = max(l1, l2)
if l > len(seq) - self.max_cut:
return l
else:
return len(seq)
def Break(self, contig):
if len(contig) < 2 * self.max_cut:
return []
l,r = self.FindLeftPos(contig.seq), self.FindRightPos(contig.seq)
return [contig.subseq(l, r)]
class NBreaker:
def __init__(self, min_N):
self.min_N = min_N
def Break(self, contig):
result = []
last_break = 0;
pos = 0
while(pos < len(contig) and contig[pos] == 'N'):
pos += 1
while pos <len(contig):
rpos = pos
while(rpos < len(contig) and contig[rpos] == 'N'):
rpos += 1
if rpos - pos >= self.min_N:
result.append(contig.subseq(last_break, pos))
last_break = rpos
pos = max(rpos, pos + 1)
if last_break != len(contig):
result.append(contig.subseq(last_break, len(contig)))
return result
#if __name__ == '__main__':
# ContigBreaker(sys.argv[1], sys.argv[3], int(sys.argv[4]), int(sys.argv[5])).OutputBroken(sys.argv[2])
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