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tig-sense.py
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#!/usr/bin/env python
#################################################################################$$
# Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted (subject to the limitations in the
# disclaimer below) provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# * Neither the name of Pacific Biosciences nor the names of its
# contributors may be used to endorse or promote products derived
# from this software without specific prior written permission.
#
# NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
# GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
# BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
# OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
# CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
# USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
# OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
# SUCH DAMAGE.
#################################################################################$$
import os
import sys
import subprocess
import shlex
from pbcore.io import FastaIO
if not len(sys.argv) == 5:
sys.exit("tig-sense.py reads.fa gkpstore tigstore workingdir\n")
sequence_file = sys.argv[1]
gkp_store = sys.argv[2]
tig_store = sys.argv[3]
work_tmp_dir = sys.argv[4]
frag_id_map = {}
fmap_args = "~/sources/wgs.svn/Linux-amd64/bin/gatekeeper -tabular -dumpfragments %s > frg_id.map" % gkp_store
print "running: %s" % fmap_args
os.system(fmap_args)
with open("frg_id.map") as fmap_out:
for l in fmap_out:
"""SRR801638.26757_corrected2/1_3278 20498"""
l = l.strip().split()
if l[0] == "UID":
continue
frag_id_map[int(l[1])] = l[0]
seq_db = {}
seqF = FastaIO.FastaReader(sequence_file)
for r in seqF:
seq_db[r.name] = r.sequence
args = "~/sources/wgs.svn/Linux-amd64/bin/tigStore -g %s -t %s 1 -D unitiglist > unitiglist" % (gkp_store, tig_store )
print "running : %s" % args
os.system(args)
out = open("unitiglist")
for l in out:
l = l.strip().split()
if len(l) == 0: continue
if l[0] == "maID": continue
unitig_id = int(l[0])
read_file_name = "%s/t_reads_%07d.fa" % (work_tmp_dir, unitig_id)
read_file = open(read_file_name, "w")
tig_ref_file_name = "%s/t_ref_%07d.fa" % (work_tmp_dir, unitig_id)
tig_ref_file = open(tig_ref_file_name, "w")
frag_list_fn = "%s/frag_list_%d" % (work_tmp_dir, unitig_id)
tigStore_args = "~/sources/wgs.svn/Linux-amd64/bin/tigStore -g %s -t %s 1 -d frags -u %d > tig_id.map" % (gkp_store, tig_store, unitig_id)
frags = []
max_coor = 0
print "running: %s" % tigStore_args
os.system(tigStore_args)
with open("tig_id.map") as tig_id_map_fh:
for frag in tig_id_map_fh:
"""FRG 1453 179419,182165"""
frag = frag.strip()
if len(frag) == 0:
continue
frag = frag.replace(",", " ")
frag = frag.strip().split()
frag_id = int(frag[1])
frags.append( ( frag_id, int(frag[2]), int(frag[3]) ) )
max_coor = max( int(frag[2]), int(frag[3]), max_coor )
rMap = dict(zip("acgtACGTnN","tgcaTGCAnN"))
seq_array = ["N"] * max_coor
for frag_id, b, e in frags:
#print frag_id, b, e
rname = frag_id_map[frag_id]
sequence = seq_db[rname]
print >>read_file, ">"+rname
print >>read_file, sequence
if b < e:
for p in range(b, e):
if seq_array[p] == "N":
try:
seq_array[p] = sequence[p-b]
except:
pass
if b > e:
b, e = e, b
rseq = "".join([rMap[c] for c in sequence[::-1]])
for p in range(b, e):
if seq_array[p] == "N":
try:
seq_array[p] = rseq[p-b]
except:
pass
print >>tig_ref_file, ">unitig_%d" % unitig_id
print >>tig_ref_file, "".join(seq_array)
#print "q-sense.py r %s %s --output_dir %s --output tig_cns_%07dd --n_iter 3 --nproc 8 --min_cov 0 --max_n_reads %d" % (read_file_name,
# tig_ref_file_name,
# work_tmp_dir,
# unitig_id,
# len(frags)*2)
read_file.close()
tig_ref_file.close()
if len(frags) == 1:
os.system("cp %s %s/tig_cns_%07d.fa" % (tig_ref_file_name, work_tmp_dir, unitig_id) )
else:
os.system("q-sense.py r %s %s --output_dir %s --output tig_cns_%07d --cname uti_cns_%07d --n_iter 3 --nproc 16 --min_cov 0 --max_n_reads %d" % (read_file_name,
tig_ref_file_name, work_tmp_dir, unitig_id, unitig_id, len(frags)*2) )
os.system("rm -f %s/t_* %s/*_input*" % (work_tmp_dir, work_tmp_dir))
out.close()