def run_cluster(*data):
"""
Run seqcluster cluster to detect smallRNA clusters
"""
sample = data[0][0]
work_dir = dd.get_work_dir(sample)
out_dir = op.join(work_dir, "seqcluster", "cluster")
out_dir = op.abspath(safe_makedir(out_dir))
prepare_dir = op.join(work_dir, "seqcluster", "prepare")
bam_file = op.join(work_dir, "align", "seqs.bam")
cluster_dir = _cluster(bam_file, prepare_dir, out_dir, dd.get_ref_file(sample), dd.get_srna_gtf_file(sample))
sample["report"] = _report(sample, dd.get_ref_file(sample))
sample["seqcluster"] = out_dir
out_mirna = _make_isomir_counts(data, out_dir=op.join(work_dir, "mirbase"))
if out_mirna:
sample = dd.set_mirna_counts(sample, out_mirna[0])
sample = dd.set_isomir_counts(sample, out_mirna[1])
out_novel = _make_isomir_counts(data, "seqbuster_novel", op.join(work_dir, "mirdeep2"), "_novel")
novel_db = mirdeep.run(data)
if out_novel:
sample = dd.set_novel_mirna_counts(sample, out_novel[0])
sample = dd.set_novel_isomir_counts(sample, out_novel[1])
data[0][0] = sample
return data
def run_cluster(*data):
"""
Run seqcluster cluster to detect smallRNA clusters
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = os.path.join(work_dir, "seqcluster", "cluster")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = op.join(work_dir, "seqcluster", "prepare")
bam_file = op.join(work_dir, "align", "seqs.bam")
cluster_dir = _cluster(bam_file, prepare_dir, out_dir, dd.get_ref_file(data[0][0]), dd.get_srna_gtf_file(data[0][0]))
report_file = _report(data[0][0], dd.get_ref_file(data[0][0]))
for sample in data:
sample[0]["seqcluster"] = out_dir
out_mirna, out_isomir = _make_isomir_counts(data)
data[0][0]["mirna_counts"] = out_mirna
data[0][0]["isomir_counts"] = out_isomir
mirdeep.run(data)
return data
def run_cluster(*data):
"""
Run seqcluster cluster to detect smallRNA clusters
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = os.path.join(work_dir, "seqcluster", "cluster")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = op.join(work_dir, "seqcluster", "prepare")
bam_file = op.join(work_dir, "align", "seqs.bam")
cluster_dir = _cluster(bam_file, prepare_dir, out_dir, dd.get_ref_file(data[0][0]), dd.get_srna_gtf_file(data[0][0]))
report_file = _report(data[0][0], dd.get_ref_file(data[0][0]))
for sample in data:
sample[0]["seqcluster"] = out_dir
out_mirna, out_isomir = _make_isomir_counts(data)
data[0][0]["mirna_counts"] = out_mirna
data[0][0]["isomir_counts"] = out_isomir
novel_db = mirdeep.run(data)
return data
def run_align(*data):
"""
Prepare data to run alignment step, only once for each project
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = op.join(work_dir, "seqcluster", "prepare")
seq_out = op.join(out_dir, "seqs.fastq")
bam_dir = op.join(work_dir, "align")
new_bam_file = op.join(bam_dir, "seqs.bam")
tools = dd.get_expression_caller(data[0][0])
if not file_exists(new_bam_file):
sample = process_alignment(data[0][0], [seq_out, None])
bam_file = dd.get_work_bam(sample[0][0])
shutil.move(bam_file, new_bam_file)
shutil.move(bam_file + ".bai", new_bam_file + ".bai")
shutil.rmtree(op.join(bam_dir, sample[0][0]["rgnames"]['sample']))
for sample in data:
sample[0]["align_bam"] = sample[0]["clean_fastq"]
if "mirdeep2" in tools:
novel_db = mirdeep.run(data)
return data
def run_align(*data):
"""
Prepare data to run alignment step, only once for each project
"""
work_dir = dd.get_work_dir(data[0][0])
out_dir = op.join(work_dir, "seqcluster", "prepare")
seq_out = op.join(out_dir, "seqs.fastq")
bam_dir = op.join(work_dir, "align")
new_bam_file = op.join(bam_dir, "seqs.bam")
tools = dd.get_expression_caller(data[0][0])
if not file_exists(new_bam_file):
sample = process_alignment(data[0][0], [seq_out, None])
bam_file = dd.get_work_bam(sample[0][0])
shutil.move(bam_file, new_bam_file)
shutil.move(bam_file + ".bai", new_bam_file + ".bai")
shutil.rmtree(op.join(bam_dir, sample[0][0]["rgnames"]['sample']))
for sample in data:
# sample[0]["align_bam"] = sample[0]["clean_fastq"]
sample[0]["cluster_bam"] = new_bam_file
if "mirdeep2" in tools:
novel_db = mirdeep.run(data)
return data
