def make_index(self): if not os.access(self.outdir, os.W_OK): mksymlink(self.files, os.path.join(self.indexdir, self.filename)) files = os.path.join(self.indexdir, self.filename) else: files = self.files return files
def make_index(self):
if not os.access(self.outdir, os.W_OK):
mksymlink(self.files, os.path.join(self.indexdir, self.filename))
files = os.path.join(self.indexdir, self.filename)
else:
files = self.files
return files
def Step1_Filter(self):
"""
Step1 filter adapter, QC
"""
filter_tools = SOAPnuke()
parameters = dict(((i, j) for i, j in self.conf.items('Filter Parameter') if j))
parameters['clean_fq_type'] = self.conf.get('Sequencing data', 'outputQualitySystem') or 'sanger'
parameters['qual_sys'] = self.conf.get('Sequencing data', 'qualitySystem') or 'illumina'
parameters['seq_type'] = self.conf.get('Sequencing data', 'fqnameType') or 'new'
for lane_number, fastq in self.messages.fq.SequenceData.iteritems():
command = list()
lane_name = '%s.lane.%d' % (self.sample, lane_number)
s_out = os.path.join(self.workdir.Script, "Step1.Filter.{0}.sh".format(lane_name))
bash = BASH(self.sample, s_out, self.log)
symdir = os.path.join(self.workdir.RawData, lane_name)
outdir = os.path.join(self.workdir.CleanData, lane_name)
qcdir = os.path.join(self.workdir.QC, lane_name)
parameters['outdir'] = outdir
if not os.path.exists(symdir):
os.makedirs(symdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
if not os.path.exists(qcdir):
os.makedirs(qcdir)
parameters['fq1'] = fastq[0][0]
parameters['clean_fq1'] = "%s.lane.%d.clean.1.fq.gz" % (self.sample, lane_number)
mksymlink(parameters['fq1'], os.path.join(symdir, os.path.basename(parameters['fq1'])))
if fastq[0][1]:
parameters['adapter1'] = fastq[0][1]
mksymlink(parameters['adapter1'], os.path.join(symdir, os.path.basename(parameters['adapter1'])))
else:
parameters['adapter1'] = None
if len(fastq) == 2:
parameters['fq2'] = fastq[1][0]
mksymlink(parameters['fq2'], os.path.join(symdir, os.path.basename(parameters['fq2'])))
parameters['clean_fq2'] = "%s.lane.%d.clean.2.fq.gz" % (self.sample, lane_number)
if fastq[1][1]:
parameters['adapter2'] = fastq[1][1]
mksymlink(parameters['adapter2'], os.path.join(symdir, os.path.basename(parameters['adapter2'])))
else:
parameters['adapter2'] = None
command.append(bash.stat_command_formact(filter_tools.filter(**parameters),
'Step1 filter lane %d' % lane_number))
command.append("mv %s/*.txt %s" % (outdir, qcdir))
bash.write(bash.bash_header_and_foot(command, 'Step1 filter lane %d' % lane_number))
bash.close()
def Step1_Filter(self):
"""
Step1 filter adapter, QC
"""
filter_tools = SOAPnuke()
parameters = dict(
((i, j) for i, j in self.conf.items('Filter Parameter') if j))
parameters['clean_fq_type'] = self.conf.get(
'Sequencing data', 'outputQualitySystem') or 'sanger'
parameters['qual_sys'] = self.conf.get('Sequencing data',
'qualitySystem') or 'illumina'
parameters['seq_type'] = self.conf.get('Sequencing data',
'fqnameType') or 'new'
for lane_number, fastq in self.messages.fq.SequenceData.iteritems():
command = list()
lane_name = '%s.lane.%d' % (self.sample, lane_number)
s_out = os.path.join(self.workdir.Script,
"Step1.Filter.{0}.sh".format(lane_name))
bash = BASH(self.sample, s_out, self.log)
symdir = os.path.join(self.workdir.RawData, lane_name)
outdir = os.path.join(self.workdir.CleanData, lane_name)
qcdir = os.path.join(self.workdir.QC, lane_name)
parameters['outdir'] = outdir
if not os.path.exists(symdir):
os.makedirs(symdir)
if not os.path.exists(outdir):
os.makedirs(outdir)
if not os.path.exists(qcdir):
os.makedirs(qcdir)
parameters['fq1'] = fastq[0][0]
parameters['clean_fq1'] = "%s.lane.%d.clean.1.fq.gz" % (
self.sample, lane_number)
mksymlink(
parameters['fq1'],
os.path.join(symdir, os.path.basename(parameters['fq1'])))
if fastq[0][1]:
parameters['adapter1'] = fastq[0][1]
mksymlink(
parameters['adapter1'],
os.path.join(symdir,
os.path.basename(parameters['adapter1'])))
else:
parameters['adapter1'] = None
if len(fastq) == 2:
parameters['fq2'] = fastq[1][0]
mksymlink(
parameters['fq2'],
os.path.join(symdir, os.path.basename(parameters['fq2'])))
parameters['clean_fq2'] = "%s.lane.%d.clean.2.fq.gz" % (
self.sample, lane_number)
if fastq[1][1]:
parameters['adapter2'] = fastq[1][1]
mksymlink(
parameters['adapter2'],
os.path.join(symdir,
os.path.basename(parameters['adapter2'])))
else:
parameters['adapter2'] = None
command.append(
bash.stat_command_formact(filter_tools.filter(**parameters),
'Step1 filter lane %d' %
lane_number))
command.append("mv %s/*.txt %s" % (outdir, qcdir))
bash.write(
bash.bash_header_and_foot(command, 'Step1 filter lane %d' %
lane_number))
bash.close()