def _generate_demultiplexed_fastq_demux(self, mtime):
"""Modularity helper"""
# An artifact will hold only one file of type
# `preprocessed_demux`. Thus, we only use the first one
# (the only one present)
ar = self.artifact
demux = [
path for _, path, ftype in ar.filepaths
if ftype == 'preprocessed_demux'
][0]
demux_samples = set()
with open_file(demux) as demux_fh:
if not isinstance(demux_fh, File):
error_msg = ("'%s' doesn't look like a demux file" % demux)
LogEntry.create('Runtime', error_msg)
raise EBISubmissionError(error_msg)
for s, i in to_per_sample_ascii(demux_fh,
self.prep_template.keys()):
sample_fp = self.sample_demux_fps[s]
wrote_sequences = False
with GzipFile(sample_fp, mode='w', mtime=mtime) as fh:
for record in i:
fh.write(record)
wrote_sequences = True
if wrote_sequences:
demux_samples.add(s)
else:
del (self.samples[s])
del (self.samples_prep[s])
del (self.sample_demux_fps[s])
remove(sample_fp)
return demux_samples
def _generate_demultiplexed_fastq_demux(self, mtime):
"""Modularity helper"""
# An artifact will hold only one file of type
# `preprocessed_demux`. Thus, we only use the first one
# (the only one present)
ar = self.artifact
demux = [path for _, path, ftype in ar.filepaths
if ftype == 'preprocessed_demux'][0]
demux_samples = set()
with open_file(demux) as demux_fh:
if not isinstance(demux_fh, File):
error_msg = (
"'%s' doesn't look like a demux file" % demux)
LogEntry.create('Runtime', error_msg)
raise EBISubmissionError(error_msg)
for s, i in to_per_sample_ascii(demux_fh,
self.prep_template.keys()):
sample_fp = self.sample_demux_fps[s]
wrote_sequences = False
with GzipFile(sample_fp, mode='w', mtime=mtime) as fh:
for record in i:
fh.write(record)
wrote_sequences = True
if wrote_sequences:
demux_samples.add(s)
else:
del(self.samples[s])
del(self.samples_prep[s])
del(self.sample_demux_fps[s])
remove(sample_fp)
return demux_samples
