def mapReadsWithTophat(infiles, outfile):
"""map reads with tophat
"""
inifile, infile = infiles
local_params = P.loadParameters(inifile)
job_options = "-l mem_free=16G"
job_threads = PARAMS["tophat_threads"]
tmpfile = P.getTempFilename(".")
# qualfile = P.snip(infile, "csfasta.gz" ) + "qual.gz"
"""
gunzip < %(infile)s > %(tmpfile)s.csfasta;
checkpoint;
gunzip < %(qualfile)s > %(tmpfile)s.qual;
checkpoint;
"""
statement = """
zcat %(infile)s
| python %(scriptsdir)s/fastq2solid.py
--method=change-format --target-format=integer
--pattern-identifier="%(tmpfile)s.%%s" >& %(outfile)s.log;
checkpoint;
tophat --output-dir %(outfile)s.dir
--num-threads %(tophat_threads)s
--library-type %(tophat_library_type)s
--color
--quals
--integer-quals
%(tophat_options)s
%(tophat_genome_dir)s/%(genome)s_cs
%(tmpfile)s.csfasta %(tmpfile)s.qual
>> %(outfile)s.log;
checkpoint;
mv %(outfile)s.dir/accepted_hits.bam %(outfile)s;
checkpoint;
samtools index %(outfile)s;
checkpoint;
rm -f %(tmpfile)s.csfasta %(tmpfile)s.qual
"""
# use local parameters to overwrite default ones.
P.run(**local_params)
os.unlink(tmpfile)
def mapReadsWithTophat(infiles, outfile):
'''map reads with tophat
'''
inifile, infile = infiles
local_params = P.loadParameters(inifile)
job_options = "-l mem_free=16G"
job_threads = PARAMS["tophat_threads"]
tmpfile = P.getTempFilename(".")
#qualfile = P.snip(infile, "csfasta.gz" ) + "qual.gz"
'''
gunzip < %(infile)s > %(tmpfile)s.csfasta;
checkpoint;
gunzip < %(qualfile)s > %(tmpfile)s.qual;
checkpoint;
'''
statement = '''
zcat %(infile)s
| python %(scriptsdir)s/fastq2solid.py
--method=change-format --target-format=integer
--pattern-identifier="%(tmpfile)s.%%s" >& %(outfile)s.log;
checkpoint;
tophat --output-dir %(outfile)s.dir
--num-threads %(tophat_threads)s
--library-type %(tophat_library_type)s
--color
--quals
--integer-quals
%(tophat_options)s
%(tophat_genome_dir)s/%(genome)s_cs
%(tmpfile)s.csfasta %(tmpfile)s.qual
>> %(outfile)s.log;
checkpoint;
mv %(outfile)s.dir/accepted_hits.bam %(outfile)s;
checkpoint;
samtools index %(outfile)s;
checkpoint;
rm -f %(tmpfile)s.csfasta %(tmpfile)s.qual
'''
# use local parameters to overwrite default ones.
P.run(**local_params)
os.unlink(tmpfile)
