def build(self, infiles, outfiles, output_prefix):
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
outdir = os.path.join(output_prefix + ".dir")
track = os.path.basename(output_prefix)
processing_options = self.processing_options
threads = self.threads
infile1, infile2 = infiles
outfile = outfiles[0]
cmd = '''pandaseq -f %(infile1)s -r %(infile2)s
%(processing_options)s
-T %(threads)i
-U >(gzip > %(outfile)s.unpaired.gz)
-w >(gzip > %(outfile)s)
-F
-G %(output_prefix)s-pandaseq.log.bgz;
>& %(output_prefix)s-pandaseq.log;
checkpoint;
gzip %(outdir)s/*;
checkpoint;
''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
processing_options = self.processing_options
r = {33: 'sanger', 64: 'illumina', 59: 'solexa'}
quality = r[offset]
if len(infiles) == 1:
infile = infiles[0]
outfile = outfiles[0]
cmd = '''sickle se
-g %(processing_options)s
--qual-type %(quality)s
--output-file %(outfile)s
--fastq-file %(infile)s
2>>%(output_prefix)s.log
;''' % locals()
elif len(infiles) == 2:
infile1, infile2 = infiles
outfile1, outfile2 = outfiles
cmd = '''sickle pe
-g -s %(processing_options)s
--qual-type %(quality)s
-f %(infile1)s -r %(infile2)s
-o %(outfile1)s -p %(outfile2)s
2>>%(output_prefix)s.log
;''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
outdir = os.path.join(output_prefix + ".dir")
track = os.path.basename(output_prefix)
processing_options = self.processing_options
infile1, infile2 = infiles
outfile = outfiles[0]
cmd = '''flash %(infile1)s %(infile2)s
-p %(offset)s
%(processing_options)s
-o %(track)s
-d %(outdir)s
>& %(output_prefix)s-flash.log;
checkpoint;
gzip %(outdir)s/*;
checkpoint;
mv %(outdir)s/%(track)s.extendedFrags.fastq.gz %(outfile)s;
''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
outdir = os.path.join(output_prefix + ".dir")
track = os.path.basename(output_prefix)
processing_options = self.processing_options
infile1, infile2 = infiles
outfile = outfiles[0]
cmd = '''flash %(infile1)s %(infile2)s
-p %(offset)s
%(processing_options)s
-o %(track)s
-d %(outdir)s
>& %(output_prefix)s-flash.log;
checkpoint;
gzip %(outdir)s/*;
checkpoint;
mv %(outdir)s/%(track)s.extendedFrags.fastq.gz %(outfile)s;
''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
outdir = os.path.join(output_prefix + ".dir")
track = os.path.basename(output_prefix)
processing_options = self.processing_options
threads = self.threads
infile1, infile2 = infiles
outfile = outfiles[0]
cmd = '''pandaseq -f %(infile1)s -r %(infile2)s
%(processing_options)s
-T %(threads)i
-U >(gzip > %(outfile)s.unpaired.gz)
-w >(gzip > %(outfile)s)
-F
-G %(output_prefix)s-pandaseq.log.bgz;
>& %(output_prefix)s-pandaseq.log;
checkpoint;
gzip %(outdir)s/*;
checkpoint;
''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
processing_options = self.processing_options
r = {33: 'sanger', 64: 'illumina', 59: 'solexa'}
quality = r[offset]
if len(infiles) == 1:
infile = infiles[0]
outfile = outfiles[0]
cmd = '''sickle se
-g %(processing_options)s
--qual-type %(quality)s
--output-file %(outfile)s
--fastq-file %(infile)s
2>>%(output_prefix)s.log
;''' % locals()
elif len(infiles) == 2:
infile1, infile2 = infiles
outfile1, outfile2 = outfiles
cmd = '''sickle pe
-g -s %(processing_options)s
--qual-type %(quality)s
-f %(infile1)s -r %(infile2)s
-o %(outfile1)s -p %(outfile2)s
2>>%(output_prefix)s.log
;''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
processing_options = self.processing_options
assert len(infiles) == len(outfiles)
cmds = []
for infile, outfile in zip(infiles, outfiles):
cmds.append('''zcat %(infile)s
| fastx_trimmer
-Q%(offset)s
%(processing_options)s
2>> %(output_prefix)s.log
| gzip > %(outfile)s
;''' % locals())
return " checkpoint; ".join(cmds)
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
prefix = self.prefix
offset = Fastq.getOffset("sanger", raises=False)
processing_options = self.processing_options
assert len(infiles) == len(outfiles)
cmds = []
for infile, outfile in zip(infiles, outfiles):
cmds.append('''zcat %(infile)s
| fastx_trimmer
-Q%(offset)s
%(processing_options)s
2>> %(output_prefix)s.log
| gzip > %(outfile)s
;''' % locals())
return " checkpoint; ".join(cmds)
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
offset = Fastq.getOffset("sanger", raises=False)
threads = self.threads
processing_options = self.processing_options
if len(infiles) == 1:
infile = infiles[0]
outfile = outfiles[0]
cmd = '''trimmomatic SE
-threads %(threads)i
-phred%(offset)s
%(infile)s %(outfile)s
%(processing_options)s
2>> %(output_prefix)s.log
;''' % locals()
elif len(infiles) == 2:
infile1, infile2 = infiles
outfile1, outfile2 = outfiles
cmd = '''trimmomatic PE
-threads %(threads)i
-phred%(offset)s
%(infile1)s %(infile2)s
%(outfile1)s %(output_prefix)s.1.unpaired
%(outfile2)s %(output_prefix)s.2.unpaired
%(processing_options)s
2>> %(output_prefix)s.log;
checkpoint;
gzip %(output_prefix)s.*.unpaired;
''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
offset = Fastq.getOffset("sanger", raises=False)
threads = self.threads
processing_options = self.processing_options
if len(infiles) == 1:
infile = infiles[0]
outfile = outfiles[0]
cmd = '''trimmomatic SE
-threads %(threads)i
-phred%(offset)s
%(infile)s %(outfile)s
%(processing_options)s
2>> %(output_prefix)s.log
;''' % locals()
elif len(infiles) == 2:
infile1, infile2 = infiles
outfile1, outfile2 = outfiles
cmd = '''trimmomatic PE
-threads %(threads)i
-phred%(offset)s
%(infile1)s %(infile2)s
%(outfile1)s %(output_prefix)s.1.unpaired
%(outfile2)s %(output_prefix)s.2.unpaired
%(processing_options)s
2>> %(output_prefix)s.log;
checkpoint;
gzip %(output_prefix)s.*.unpaired;
''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
offset = Fastq.getOffset("sanger", raises=False)
processing_options = self.processing_options
if len(infiles) == 1:
infile = infiles[0]
outfile = outfiles[0]
outdir = os.path.dirname(outfile)
trim_out = "%s/%s_trimmed.fq.gz" % (
outdir, infile.replace(".fastq.gz", ""))
cmd = '''trim_galore %(processing_options)s
--phred%(offset)s
--output_dir %(outdir)s
%(infile)s
2>>%(output_prefix)s.log;
mv %(trim_out)s %(outfile)s;
''' % locals()
outfiles = (outfile, )
elif len(infiles) == 2:
infile1, infile2 = infiles
outfile1, outfile2 = outfiles
outdir = os.path.dirname(outfile1)
cmd = '''trim_galore %(processing_options)s
--paired
--phred%(offset)s
--output_dir %(outdir)s
%(infile1)s %(infile2)s
2>>%(output_prefix)s.log;
mv %(outdir)s/%(infile1)s_val_1.fq.gz %(outfile1)s;
mv %(outdir)s/%(infile2)s_val_2.fq.gz %(outfile2)s;
''' % locals()
return cmd
def build(self, infiles, outfiles, output_prefix):
assert len(infiles) == len(outfiles)
assert len(infiles) in (1, 2)
offset = Fastq.getOffset("sanger", raises=False)
processing_options = self.processing_options
if len(infiles) == 1:
infile = infiles[0]
outfile = outfiles[0]
trim_out = "%s_trimmed.fq.gz" % (output_prefix)
cmd = '''trim_galore %(processing_options)s
--phred%(offset)s
--output_dir %(outdir)s
%(infile)s
2>>%(output_prefix)s.log;
mv %(trim_out)s %(outfile)s;
''' % locals()
outfiles = (outfile,)
elif self.num_files == 2:
infile1, infile2 = infiles
outfile1, outfile2 = outfiles
cmd = '''trim_galore %(processing_options)s
--paired
--phred%(offset)s
--output_dir %(outdir)s
%(infile1)s %(infile2)s
2>>%(output_prefix)s.log;
mv %(infile1)s_val_1.fq.gz %(outfile1)s;
mv %(infile2)s_val_2.fq.gz %(outfile2)s;
''' % locals()
return cmd
def processReads(infiles, outfile):
'''process reads.'''
infile, contaminant_file = infiles
do_sth = False
to_cluster = True
infile2 = checkPairs(infile)
if infile2:
track = P.snip(outfile, ".fastq.1.gz")
outfile2 = P.snip(outfile, ".fastq.1.gz") + ".fastq.2.gz"
else:
track = P.snip(outfile, ".fastq.gz")
if PARAMS["process_combine_reads"]:
E.warn(
"combining reads cannot be can not be combined with other processing for paired ended reads"
)
if not infile2: raise IOError("must have paired data to combine reads")
read_len, frag_len, frag_stdev = PARAMS["combine_reads_read_length"], \
PARAMS["combine_reads_fragment_length"], \
PARAMS["combine_reads_fragment_length_stdev"]
fragment_options = " ".join(map(str, [read_len, frag_len, frag_stdev]))
if PARAMS["combine_reads_max_overlap"]:
E.warn(
"if specifying --max-overlap read and fragment length options will be ignored"
)
max_overlap = "--max-overlap=%i" % PARAMS[
"combine_reads_max_overlap"]
fragment_options = ""
elif not PARAMS["combine_reads_max_overlap"] and len(
fragment_options.strip().split(" ")) < 3:
E.warn(
"have not specified --read-len, --frag-len, --frag-len-stddev: default --max-overlap used"
)
max_overlap = ""
fragment_options = ""
elif PARAMS["combine_reads_read_length"] and PARAMS[
"combine_reads_fragment_length"] and PARAMS[
"combine_reads_fragment_length_stdev"]:
if PARAMS["combine_reads_max_overlap"]:
E.warn(
"--max-overlap will override the specified read and fragment length options"
)
max_overlap = ""
fragment_options = """--read-len=%(read_len)i
--fragment-len=%(frag_len)i
--fragment-len-stddev=%(frag_stdev)i""" % locals(
)
else:
max_overlap = ""
fragment_options = ""
if not PARAMS["combine_reads_min_overlap"]:
min_overlap = ""
else:
min_overlap = "--min-overlap=%i" % PARAMS[
"combine_reads_min_overlap"]
if not PARAMS["combine_reads_threads"]:
threads = ""
else:
threads = "--threads=%i" % PARAMS["combine_reads_threads"]
if not PARAMS["combine_reads_phred_offset"]:
phred_offset = ""
else:
phred_offset = "--phred-offset=%i" % PARAMS[
"combine_reads_phred_offset"]
if not PARAMS["combine_reads_max_mismatch_density"]:
max_mismatch_density = ""
else:
max_mismatch_density = "--max-mismatch-density=%f" % PARAMS[
"combine_reads_max_mismatch_density"]
statement = '''flash
%(min_overlap)s
%(max_overlap)s
%(max_mismatch_density)s
%(phred_offset)s
%(fragment_options)s
--output-prefix=%(track)s
%(threads)s
--compress
%(infile)s %(infile2)s >> %(outfile)s.log
'''
P.run()
if PARAMS["combine_reads_concatenate"]:
infiles = " ".join([
track + x for x in [
".notCombined_1.fastq.gz", ".notCombined_2.fastq.gz",
".extendedFrags.fastq.gz"
]
])
statement = '''zcat %(infiles)s | gzip > %(outfile)s; rm -rf %(infiles)s'''
else:
statement = '''mv %(track)s.extendedFrags.fastq.gz %(outfile)s'''
P.run()
return
if PARAMS["process_sample"] and infile2:
E.warn(
"sampling can not be combined with other processing for paired ended reads"
)
statement = '''zcat %(infile)s
| python %(scriptsdir)s/fastq2fastq.py
--sample=%(sample_proportion)f
--pair=%(infile2)s
--outfile-pair=%(outfile2)s
--log=%(outfile)s_sample.log
| gzip
> %(outfile)s
'''
P.run()
return
# fastx does not like quality scores below 64 (Illumina 1.3 format)
# need to detect the scores and convert
format = Fastq.guessFormat(IOTools.openFile(infile), raises=False)
E.info("%s: format guess: %s" % (infile, format))
offset = Fastq.getOffset(format, raises=False)
if PARAMS["process_remove_contaminants"]:
adaptors = listAdaptors(contaminant_file)
# %(contamination_trim_type)s
s = [
'''
cutadapt
%(adaptors)s
--overlap=%(contamination_min_overlap_length)i
--format=fastq
%(contamination_options)s
<( zcat < %(infile)s )
2>> %(outfile)s_contaminants.log
'''
]
do_sth = True
else:
s = ['zcat %(infile)s']
if PARAMS["process_artifacts"]:
s.append(
'fastx_artifacts_filter -Q %(offset)i -v %(artifacts_options)s 2>> %(outfile)s_artifacts.log'
)
do_sth = True
if PARAMS["process_trim"]:
s.append(
'fastx_trimmer -Q %(offset)i -v %(trim_options)s 2>> %(outfile)s_trim.log'
)
do_sth = True
# NICK - may replace fastx trimmer
if PARAMS["process_trim_quality"]:
s.append(
'fastq_quality_trimmer -Q %(offset)i -v %(trim_quality_options)s 2>> %(outfile)s_trim.log'
)
do_sth = True
if PARAMS["process_filter"]:
s.append(
'fastq_quality_filter -Q %(offset)i -v %(filter_options)s 2>> %(outfile)s_filter.log'
)
do_sth = True
if PARAMS["process_sample"]:
s.append(
'python %(scriptsdir)s/fastq2fastq.py --sample=%(sample_proportion)f --log=%(outfile)s_sample.log'
)
if not do_sth:
E.warn("no filtering specified for %s - nothing done" % infile)
return
s.append("gzip")
if not infile2:
statement = " | ".join(s) + " > %(outfile)s"
P.run()
else:
tmpfile = P.getTempFilename(".")
tmpfile1 = tmpfile + ".fastq.1.gz"
tmpfile2 = tmpfile + ".fastq.2.gz"
E.warn("processing first of pair")
# first read pair
statement = " | ".join(s) + " > %(tmpfile1)s"
P.run()
# second read pair
E.warn("processing second of pair")
infile = infile2
statement = " | ".join(s) + " > %(tmpfile2)s"
P.run()
# reconcile
E.info("starting reconciliation")
statement = """python %(scriptsdir)s/fastqs2fastqs.py
--method=reconcile
--output-pattern=%(track)s.fastq.%%s.gz
%(tmpfile1)s %(tmpfile2)s
> %(outfile)s_reconcile.log"""
P.run()
os.unlink(tmpfile1)
os.unlink(tmpfile2)
os.unlink(tmpfile)
def setfastqAttr(self, infiles):
self.offset = Fastq.getOffset(self.f_format, raises=False)
def processReads( infiles, outfile ):
'''process reads.'''
infile, contaminant_file = infiles
do_sth = False
to_cluster = True
infile2 = checkPairs( infile )
if infile2:
track = P.snip( outfile, ".fastq.1.gz" )
outfile2 = P.snip( outfile, ".fastq.1.gz" ) + ".fastq.2.gz"
else:
track = P.snip( outfile, ".fastq.gz" )
if PARAMS["process_combine_reads"]:
E.warn("combining reads cannot be can not be combined with other processing for paired ended reads")
if not infile2: raise IOError("must have paired data to combine reads")
read_len, frag_len, frag_stdev = PARAMS["combine_reads_read_length"], \
PARAMS["combine_reads_fragment_length"], \
PARAMS["combine_reads_fragment_length_stdev"]
fragment_options = " ".join(map(str,[read_len, frag_len, frag_stdev]))
if PARAMS["combine_reads_max_overlap"]:
E.warn("if specifying --max-overlap read and fragment length options will be ignored")
max_overlap="--max-overlap=%i" % PARAMS["combine_reads_max_overlap"]
fragment_options = ""
elif not PARAMS["combine_reads_max_overlap"] and len(fragment_options.strip().split(" ")) < 3:
E.warn("have not specified --read-len, --frag-len, --frag-len-stddev: default --max-overlap used")
max_overlap = ""
fragment_options = ""
elif PARAMS["combine_reads_read_length"] and PARAMS["combine_reads_fragment_length"] and PARAMS["combine_reads_fragment_length_stdev"]:
if PARAMS["combine_reads_max_overlap"]:
E.warn("--max-overlap will override the specified read and fragment length options")
max_overlap = ""
fragment_options = """--read-len=%(read_len)i
--fragment-len=%(frag_len)i
--fragment-len-stddev=%(frag_stdev)i""" % locals()
else:
max_overlap = ""
fragment_options = ""
if not PARAMS["combine_reads_min_overlap"]:
min_overlap = ""
else:
min_overlap = "--min-overlap=%i" % PARAMS["combine_reads_min_overlap"]
if not PARAMS["combine_reads_threads"]:
threads = ""
else:
threads = "--threads=%i" % PARAMS["combine_reads_threads"]
if not PARAMS["combine_reads_phred_offset"]:
phred_offset = ""
else:
phred_offset = "--phred-offset=%i" % PARAMS["combine_reads_phred_offset"]
if not PARAMS["combine_reads_max_mismatch_density"]:
max_mismatch_density = ""
else:
max_mismatch_density = "--max-mismatch-density=%f" % PARAMS["combine_reads_max_mismatch_density"]
statement = '''flash
%(min_overlap)s
%(max_overlap)s
%(max_mismatch_density)s
%(phred_offset)s
%(fragment_options)s
--output-prefix=%(track)s
%(threads)s
--compress
%(infile)s %(infile2)s >> %(outfile)s.log
'''
P.run()
if PARAMS["combine_reads_concatenate"]:
infiles = " ".join([track + x for x in [".notCombined_1.fastq.gz", ".notCombined_2.fastq.gz", ".extendedFrags.fastq.gz"]])
statement = '''zcat %(infiles)s | gzip > %(outfile)s; rm -rf %(infiles)s'''
else:
statement = '''mv %(track)s.extendedFrags.fastq.gz %(outfile)s'''
P.run()
return
if PARAMS["process_sample"] and infile2:
E.warn( "sampling can not be combined with other processing for paired ended reads")
statement = '''zcat %(infile)s
| python %(scriptsdir)s/fastq2fastq.py
--sample=%(sample_proportion)f
--pair=%(infile2)s
--outfile-pair=%(outfile2)s
--log=%(outfile)s_sample.log
| gzip
> %(outfile)s
'''
P.run()
return
# fastx does not like quality scores below 64 (Illumina 1.3 format)
# need to detect the scores and convert
format = Fastq.guessFormat( IOTools.openFile(infile ) , raises = False)
E.info( "%s: format guess: %s" % (infile, format))
offset = Fastq.getOffset( format, raises = False )
if PARAMS["process_remove_contaminants"]:
adaptors = listAdaptors(contaminant_file)
# %(contamination_trim_type)s
s = [ '''
cutadapt
%(adaptors)s
--overlap=%(contamination_min_overlap_length)i
--format=fastq
%(contamination_options)s
<( zcat < %(infile)s )
2>> %(outfile)s_contaminants.log
''' ]
do_sth = True
else:
s = ['zcat %(infile)s' ]
if PARAMS["process_artifacts"]:
s.append( 'fastx_artifacts_filter -Q %(offset)i -v %(artifacts_options)s 2>> %(outfile)s_artifacts.log' )
do_sth = True
if PARAMS["process_trim"]:
s.append( 'fastx_trimmer -Q %(offset)i -v %(trim_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
# NICK - may replace fastx trimmer
if PARAMS["process_trim_quality"]:
s.append( 'fastq_quality_trimmer -Q %(offset)i -v %(trim_quality_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
if PARAMS["process_filter"]:
s.append( 'fastq_quality_filter -Q %(offset)i -v %(filter_options)s 2>> %(outfile)s_filter.log')
do_sth = True
if PARAMS["process_sample"]:
s.append( 'python %(scriptsdir)s/fastq2fastq.py --sample=%(sample_proportion)f --log=%(outfile)s_sample.log' )
if not do_sth:
E.warn( "no filtering specified for %s - nothing done" % infile )
return
s.append( "gzip" )
if not infile2:
statement = " | ".join( s ) + " > %(outfile)s"
P.run()
else:
tmpfile = P.getTempFilename(".")
tmpfile1 = tmpfile + ".fastq.1.gz"
tmpfile2 = tmpfile + ".fastq.2.gz"
E.warn( "processing first of pair")
# first read pair
statement = " | ".join( s ) + " > %(tmpfile1)s"
P.run()
# second read pair
E.warn( "processing second of pair")
infile = infile2
statement = " | ".join( s ) + " > %(tmpfile2)s"
P.run()
# reconcile
E.info("starting reconciliation" )
statement = """python %(scriptsdir)s/fastqs2fastqs.py
--method=reconcile
--output-pattern=%(track)s.fastq.%%s.gz
%(tmpfile1)s %(tmpfile2)s
> %(outfile)s_reconcile.log"""
P.run()
os.unlink( tmpfile1 )
os.unlink( tmpfile2 )
os.unlink( tmpfile )
def processReads( infiles, outfile ):
'''process reads.'''
infile, contaminant_file = infiles
do_sth = False
to_cluster = True
infile2 = checkPairs( infile )
if infile2:
track = P.snip( outfile, ".fastq.1.gz" )
outfile2 = P.snip( outfile, ".fastq.1.gz" ) + ".fastq.2.gz"
else:
track = P.snip( outfile, ".fastq.gz" )
if PARAMS["process_sample"] and infile2:
E.warn( "sampling can not be combined with other processing for paired ended reads")
statement = '''zcat %(infile)s
| python %(scriptsdir)s/fastq2fastq.py
--sample=%(sample_proportion)f
--pair=%(infile2)s
--outfile-pair=%(outfile2)s
--log=%(outfile)s_sample.log
| gzip
> %(outfile)s
'''
P.run()
return
# fastx does not like quality scores below 64 (Illumina 1.3 format)
# need to detect the scores and convert
format = Fastq.guessFormat( IOTools.openFile(infile ) , raises = False)
E.info( "%s: format guess: %s" % (infile, format))
offset = Fastq.getOffset( format, raises = False )
if PARAMS["process_remove_contaminants"]:
adaptors = listAdaptors(contaminant_file)
# %(contamination_trim_type)s
s = [ '''
cutadapt
%(adaptors)s
--overlap=%(contamination_min_overlap_length)i
--format=fastq
%(contamination_options)s
<( zcat < %(infile)s )
2>> %(outfile)s_contaminants.log
''' ]
do_sth = True
else:
s = ['zcat %(infile)s' ]
if PARAMS["process_artifacts"]:
s.append( 'fastx_artifacts_filter -Q %(offset)i -v %(artifacts_options)s 2>> %(outfile)s_artifacts.log' )
do_sth = True
if PARAMS["process_trim"]:
s.append( 'fastx_trimmer -Q %(offset)i -v %(trim_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
# NICK - may replace fastx trimmer
if PARAMS["process_trim_quality"]:
s.append( 'fastq_quality_trimmer -Q %(offset)i -v %(trim_options)s 2>> %(outfile)s_trim.log' )
do_sth = True
if PARAMS["process_filter"]:
s.append( 'fastq_quality_filter -Q %(offset)i -v %(filter_options)s 2>> %(outfile)s_filter.log')
do_sth = True
if PARAMS["process_sample"]:
s.append( 'python %(scriptsdir)s/fastq2fastq.py --sample=%(sample_proportion)f --log=%(outfile)s_sample.log' )
if not do_sth:
E.warn( "no filtering specified for %s - nothing done" % infile )
return
s.append( "gzip" )
if not infile2:
statement = " | ".join( s ) + " > %(outfile)s"
P.run()
else:
tmpfile = P.getTempFilename(".")
tmpfile1 = tmpfile + ".fastq.1.gz"
tmpfile2 = tmpfile + ".fastq.2.gz"
E.warn( "processing first of pair")
# first read pair
statement = " | ".join( s ) + " > %(tmpfile1)s"
P.run()
# second read pair
E.warn( "processing second of pair")
infile = infile2
statement = " | ".join( s ) + " > %(tmpfile2)s"
P.run()
# reconcile
E.info("starting reconciliation" )
statement = """python %(scriptsdir)s/fastqs2fastqs.py
--method=reconcile
--output-pattern=%(track)s.fastq.%%i.gz
%(tmpfile1)s %(tmpfile2)s
> %(outfile)s_reconcile.log"""
P.run()
os.unlink( tmpfile1 )
os.unlink( tmpfile2 )
os.unlink( tmpfile )
