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;
gzip %(outdir)s/*;
''' % 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;
gzip %(outdir)s/*;
mv %(outdir)s/%(track)s.extendedFrags.fastq.gz %(outfile)s;
''' % 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 " ; ".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;
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
