def _make_isomir_counts(data, srna_type="seqbuster", out_dir=None, stem=""):
"""
Parse miraligner files to create count matrix.
"""
work_dir = dd.get_work_dir(data[0][0])
if not out_dir:
out_dir = op.join(work_dir, "mirbase")
out_novel_isomir = append_stem(op.join(out_dir, "counts.tsv"), stem)
out_novel_mirna = append_stem(op.join(out_dir, "counts_mirna.tsv"), stem)
logger.debug("Create %s count data at %s." % (srna_type, out_dir))
if file_exists(out_novel_mirna):
return [out_novel_mirna, out_novel_isomir]
out_dts = []
for sample in data:
if sample[0].get(srna_type):
miraligner_fn = sample[0][srna_type]
reads = _read_miraligner(miraligner_fn)
if reads:
out_file, dt, dt_pre = _tab_output(reads, miraligner_fn + ".back", dd.get_sample_name(sample[0]))
out_dts.append(dt)
else:
logger.debug("WARNING::%s has NOT miRNA annotated for %s. Check if fasta files is small or species value." % (dd.get_sample_name(sample[0]), srna_type))
if out_dts:
out_files = _create_counts(out_dts, out_dir)
out_files = [move_safe(out_files[0], out_novel_isomir), move_safe(out_files[1], out_novel_mirna)]
return out_files
else:
logger.debug("WARNING::any samples have miRNA annotated for %s. Check if fasta files is small or species value." % srna_type)
def _make_isomir_counts(data):
"""
Parse miraligner files to create count matrix.
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = os.path.join(work_dir, "mirbase")
out_dts = []
for sample in data:
miraligner_fn = sample[0]["seqbuster"]
reads = _read_miraligner(miraligner_fn)
if reads:
out_file, dt = _tab_output(reads, miraligner_fn + ".back",
dd.get_sample_name(sample[0]))
out_dts.append(dt)
else:
logger.log(
"WARNING::%s has NOT miRNA annotated. Check if fasta files is small or species value."
% dd.get_sample_name(sample[0]))
if out_dts:
out_files = _create_counts(out_dts, out_dir)
else:
logger.log(
"WARNING::any samples have miRNA annotated. Check if fasta files is small or species value."
)
return out_files
def _make_isomir_counts(data):
"""
Parse miraligner files to create count matrix.
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = os.path.join(work_dir, "mirbase")
out_dts = []
for sample in data:
miraligner_fn = sample[0]["seqbuster"]
reads = _read_miraligner(miraligner_fn)
if reads:
out_file, dt = _tab_output(reads, miraligner_fn + ".back", dd.get_sample_name(sample[0]))
out_dts.append(dt)
else:
logger.log("WARNING::%s has NOT miRNA annotated. Check if fasta files is small or species value." % dd.get_sample_name(sample[0]))
if out_dts:
out_files = _create_counts(out_dts, out_dir)
else:
logger.log("WARNING::any samples have miRNA annotated. Check if fasta files is small or species value.")
return out_files