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# test splitting of reads aligning across consecutive reference
# sequences. This is relevant when the number of reference sequences >
# SMALT_MAX_REFSEQ_NUM (= 512). In that case the reads are aligned
# against concatenated reference sequences and the index of the
# reference sequence (i.e. name, length) is worked out a-posteriory.
# Splitting the alignment string my result in fragments ending in
# mismatches etc. which have to be cleaned up.
#############################################################################
#############################################################################
# #
# Copyright (C) 2013 - 2014 Genome Research Ltd. #
# #
# Author: Hannes Ponstingl (hp3@sanger.ac.uk) #
# #
# This file is part of SMALT. #
# #
# SMALT is free software: you can redistribute it and/or modify it under #
# the terms of the GNU General Public License as published by the Free #
# Software Foundation, either version 3 of the License, or (at your #
# option) any later version. #
# #
# This program is distributed in the hope that it will be useful, but #
# WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU #
# General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License along #
# with this program. If not, see <http://www.gnu.org/licenses/>. #
# #
#############################################################################
#############################################################################
from sys import path
path.append('../misc') # find SAM.py
PROGNAM = "./smalt_Xali_test"
PROGNAM_REVCOMP = "./sequenceReverseComplement_test"
REFSEQ = (
"ggggaaacagttgccttctcagaaccgtgcggacttataaaaaatgaaagtcagaaactt"\
"gctgctctcggtgatccgtgcggaagtgcaagtgaaaaacgtttttctaaagaacgtgtc"\
"gatgaatatgataagaaaaaaataaaatgtagtaatagtgaaggagcttgcgctccatat",
"agacgattgcacgtatgcgacaaaaatatggtaaaaatggacacaaataatgatagtaaa"\
"gctaaacatgatttattgttggatgtgtgtcttgcagcaaagtatgaaggagagtcatta",
"aaaacatatcgtgcacaatatgatgaacaatatccttcttctgtttctacttttacaatg"\
"tgtactatgttagcacgaagttttgccgatataggtgatattgtcagaggaagagatttg"\
"tatcgtggcaatagaaagaaaaatgaaacaaaaacagaaagagaaaaattagatgataag"
)
READS = (
"aagaaaaaaataaaatgtagtaatagtgaaggagcttgcgctccatat"\
"agacgattgcacgtatgcgacaaaaatatggtaaaaatgg",
"aagaaaaaaataaaatgtagtaatagtgaaggagcttgcgctccatac"\
"agacgattgcacgtatgcgacaaaaatatggtaaaaatgg",
"aagaaaaaaataaaatgtagtaatagtgaaggagcttgcgctccttgc"\
"agacgattgcacgtatgcgacaaaaatatggtaaaaatgg",
"tgtagtaatagtgaaggagcttgcgctccatat"\
"cgacgattgcacgtatgcgacaaaaatatggtaaaaatgg",
"tgtagtaatagtgaaggagcttgcgctccatat"\
"cgcgattgcacgtatgcgacaaaaatatggtaaaaatgg",
)
# ref no, pos, cigar, edit distance
RESULTS = ((1, 133, "48M40S", 0),
(1, 133, "47M41S", 0),
(1, 133, "44M1X1M42S", 1),
(2, 2, "34S39M", 0),
(2, 2, "34S1M1D37M", 1))
TMPFIL_PREFIX = "tmp"
KMER = 11
NSKIP = 2
from re import compile
REFNAMNO = compile("^\S+_(\d+)")
def asFASTA(seqnamprefix, sequences):
oustr = ""
ctr = 1
for seq in sequences:
oustr = oustr + ">%s_%i\n%s\n" % (seqnamprefix, ctr, seq)
ctr = ctr + 1
return oustr
def makeFASTAfile(df, prefix, sequences):
from testdata import openFile
filnam = df.addTMP("%s%s.fa" % (TMPFIL_PREFIX, prefix))
oufil = openFile(filnam, 'w')
oustr = asFASTA(prefix, sequences)
oufil.write(oustr)
oufil.close()
return filnam
def reverseComplement(df, fastq_name_F, fastq_name_R):
tup = (PROGNAM_REVCOMP,
fastq_name_F,
fastq_name_R)
df.call(tup, "reverse complement failed")
return
def smalt_index(df, index_name, fasta_name, kmer, nskip):
tup = (PROGNAM, 'index',
'-k', '%i' % (int(kmer)),
'-s', '%i' % (int(nskip)),
index_name,
fasta_name)
df.call(tup, "when indexing")
def smalt_map(df, oufilnam, indexnam, readfil, option=[]):
tup = [PROGNAM, 'map', '-f', 'sam:x', '-o', oufilnam]
if option:
tup.extend(option)
tup.extend([indexnam, readfil])
df.call(tup, "when mapping")
def refnoFromNam(refnam):
m = REFNAMNO.search(refnam)
return int(m.group(1))
def checkSAM(df, filnam_sam, results):
from SAM import Sam, openFile
sam = Sam()
infil = openFile(filnam_sam, 'r')
for res in results:
sam.next(infil)
if not sam.ok:
df.exitErr("ERROR: Could not parse file '%s'" % (filnam_sam))
refno = refnoFromNam(sam.rname)
if refno != res[0]:
df.exitErr("ERROR: wrong reference sequence %i '%s' (target: %i)" % \
(refno, sam.rname, res[0]))
if sam.pos != res[1]:
df.exitErr("ERROR: wrong reference position %i (target:%i)" % (sam.pos, res[1]))
if sam.cigar != res[2]:
df.exitErr("ERROR: wrong CIGAR string '%s' (target:'%s')" % (sam.cigar, res[2]))
(typ, fld) = sam.tags["NM"]
edist = int(fld)
if edist != res[3]:
df.exitErr("ERROR: wrong edit distance %i (target: %i)" % (edist, res[3]))
infil.close()
return
if __name__ == '__main__':
from testdata import DataFiles
df = DataFiles()
indexnam = df.addIndex(TMPFIL_PREFIX)
reffilnam = makeFASTAfile(df, "REF", REFSEQ)
readfilnam = makeFASTAfile(df, "READ", READS)
rc_readfilnam = df.addTMP(TMPFIL_PREFIX + "RC.fa")
samfilnam = df.addTMP(TMPFIL_PREFIX + ".sam")
rc_samfilnam = df.addTMP(TMPFIL_PREFIX + "RC.sam")
smalt_index(df, indexnam, reffilnam, KMER, NSKIP)
smalt_map(df, samfilnam, indexnam, readfilnam)
checkSAM(df, samfilnam, RESULTS)
reverseComplement(df, readfilnam, rc_readfilnam)
smalt_map(df, rc_samfilnam, indexnam, rc_readfilnam)
checkSAM(df, samfilnam, RESULTS)
df.cleanup()
exit(0)
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