def set_read_fasta(self, read_fasta_file):
self.reads_set = True
gfr = SequenceBasics.GenericFastaFileReader(read_fasta_file)
self.reads = {}
while True:
e = gfr.read_entry()
if not e: break
if e['name'] in self.reads:
sys.stderr.write(
"Warning duplicate name in fasta file, could be big problems on sequence assignment.\n"
)
self.reads[e['name']] = e['seq'].upper()
gfr.close()
return
def main():
parser = argparse.ArgumentParser()
parser.add_argument("bwa_bam",
help="BAMFILE or - for sam streamed to stdin")
parser.add_argument('-o',
'--output',
help="OUTFILE or if not set use STDOUT")
group1 = parser.add_mutually_exclusive_group(required=True)
group1.add_argument("--query_fasta", help="FASTA for query sequences")
group1.add_argument("--query_fastq", help="FASTQ for query sequences")
parser.add_argument("--ref",
required=True,
help="FASTA for reference genome")
parser.add_argument(
"-S",
"--size",
help="linux sort option S, in kb if units not specified")
group2 = parser.add_mutually_exclusive_group()
group2.add_argument("--tempdir",
default='/tmp',
help="DIR to store a temp directory")
group2.add_argument("--specific_tempdir",
help="Exact DIR to work in, is not deleted")
parser.add_argument(
"--get_all_alignments",
action='store_true',
help="Be exhaustive in retrieving secondary and chimeric alignments")
args = parser.parse_args()
# Manage your tempdir
# put it into args.tempdir
if not args.specific_tempdir:
rnum = random.randint(1, 100000000)
args.tempdir = args.tempdir.rstrip('/') + '/weirathe.' + str(rnum)
else:
args.tempdir = args.specific_tempdir.rstrip('/')
if not os.path.exists(args.tempdir):
os.makedirs(args.tempdir)
inf = sys.stdin
if args.bwa_bam != '-':
p1 = subprocess.Popen(("samtools view " + args.bwa_bam).split(),
stdout=subprocess.PIPE)
inf = p1.stdout
# 1. Now we can start the process. First convert the sam to a psl
cmd = "sam_to_psl.py -"
if args.get_all_alignments:
cmd += " --get_all_alignments"
#No matter what we don't need to see the exact same alignment more than once
cmd += " | sort -T " + args.tempdir
if args.size:
cmd += " -S " + args.size
cmd += " | uniq"
#Sort the alignment based on query name
cmd += " | sort_psl.py - --tempdir " + args.tempdir
if args.size:
cmd += " -S " + args.size
#Put the fragmented alignments together
cmd += " | defragment_PSL_alignments.py - | sort_psl.py - --tempdir " + args.tempdir + " -o " + args.tempdir + "/1.psl"
if args.size:
cmd += " -S " + args.size
p2 = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE)
for line in inf:
p2.stdin.write(line)
p2.communicate()
if args.bwa_bam != '-':
p1.communicate()
# 2. Get a sorted fasta file
cmd = "sort_fasta.py - --tempdir " + args.tempdir + " -o " + args.tempdir + '/2.query.fa'
if args.size:
cmd += " -S " + args.size
p3 = subprocess.Popen(cmd.split(), stdin=subprocess.PIPE)
if args.query_fasta:
gfr = SequenceBasics.GenericFastaFileReader(args.query_fasta)
else:
gfr = SequenceBasics.GenericFastqFileReader(args.query_fastq)
while True:
e = gfr.read_entry()
if not e: break
p3.stdin.write('>' + e['name'] + "\n" + e['seq'] + "\n")
p3.communicate()
gfr.close()
# 3. Fix the psl and output the results
of = sys.stdout
if args.output:
of = open(args.output, 'w')
cmd = "fix_psl_stats.py " + args.tempdir + '/1.psl ' + args.ref + ' ' + args.tempdir + '/2.query.fa | sort_psl.py - --tempdir ' + args.tempdir
if args.size:
cmd += " -S " + args.size
p4 = subprocess.Popen(cmd, shell=True, stdout=of)
p4.communicate()
# Clean up your temporary directory if you aren't in a specific one.
if not args.specific_tempdir:
rmtree(args.tempdir)
return
