def run_cluster(*data):
"""
Run seqcluster cluster to detect smallRNA clusters
"""
sample = data[0][0]
tools = dd.get_expression_caller(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 = data[0][0]["work_bam"]
if "seqcluster" in tools:
sample["seqcluster"] = _cluster(bam_file,
data[0][0]["seqcluster_prepare_ma"],
out_dir, dd.get_ref_file(sample),
dd.get_srna_gtf_file(sample))
sample["report"] = _report(sample, dd.get_ref_file(sample))
if "mirge" in tools:
sample["mirge"] = mirge.run(data)
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")
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
data = spikein.combine_spikein(data)
return data
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
"""
out_dir = os.path.join(dd.get_work_dir(data[0]), "seqcluster", "cluster")
out_dir = os.path.abspath(safe_makedir(out_dir))
prepare_dir = op.join(dd.get_work_dir(data[0]), "seqcluster", "prepare")
bam_file = op.join(dd.get_work_dir(data[0]), "align", "seqs.bam")
cluster_dir = _cluster(bam_file, prepare_dir, out_dir, dd.get_ref_file(data[0]), dd.get_srna_gtf_file(data[0]))
for sample in data:
sample["seqcluster"] = out_dir
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
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
# from bcbio.srna import mirdeep
# mirdeep.run(data)
return data
def run_cluster(*data):
"""
Run seqcluster cluster to detect smallRNA clusters
"""
sample = data[0][0]
tools = dd.get_expression_caller(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 = data[0][0]["work_bam"]
if "seqcluster" in tools:
sample["seqcluster"] = _cluster(bam_file, data[0][0]["seqcluster_prepare_ma"], out_dir, dd.get_ref_file(sample), dd.get_srna_gtf_file(sample))
sample["report"] = _report(sample, dd.get_ref_file(sample))
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")
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
return data