def sample_summary(bam_file, data, out_dir):
"""Run RNA-SeQC on a single RNAseq sample, writing to specified output directory.
"""
metrics_file = os.path.join(out_dir, "metrics.tsv")
if not file_exists(metrics_file):
config = data["config"]
ref_file = data["sam_ref"]
genome_dir = os.path.dirname(os.path.dirname(ref_file))
gtf_file = config_utils.get_transcript_gtf(genome_dir)
rna_file = config_utils.get_rRNA_sequence(genome_dir)
sample_file = os.path.join(safe_makedir(out_dir), "sample_file.txt")
_write_sample_id_file(data, bam_file, sample_file)
runner = rnaseqc_runner_from_config(config)
bam.index(bam_file, config)
single_end = bam.is_paired(bam_file)
runner.run(sample_file, ref_file, rna_file, gtf_file, out_dir, single_end)
return _parse_rnaseqc_metrics(metrics_file, data["name"][-1])
def sample_summary(samples):
sample_config = samples[0]
config = sample_config[0]["config"]
work_dir = sample_config[0]["dirs"]["work"]
ref_file = sample_config[0]["sam_ref"]
genome_dir = os.path.dirname(os.path.dirname(ref_file))
gtf_file = config_utils.get_transcript_gtf(genome_dir)
rna_file = config_utils.get_rRNA_sequence(genome_dir)
out_dir = safe_makedir(os.path.join(work_dir, "qc", "rnaseqc"))
sample_file = os.path.join(out_dir, "sample_file.txt")
_write_sample_id_file(samples, sample_file)
_index_samples(samples)
runner = rnaseqc_runner_from_config(config)
single_end = is_paired(sample_config[0]["work_bam"])
runner.run(sample_file, ref_file, rna_file, gtf_file, out_dir, single_end)
return samples
def sample_summary(bam_file, data, out_dir):
"""Run RNA-SeQC on a single RNAseq sample, writing to specified output directory.
"""
metrics_file = os.path.join(out_dir, "metrics.tsv")
if not file_exists(metrics_file):
config = data["config"]
ref_file = data["sam_ref"]
genome_dir = os.path.dirname(os.path.dirname(ref_file))
gtf_file = config_utils.get_transcript_gtf(genome_dir)
rna_file = config_utils.get_rRNA_sequence(genome_dir)
sample_file = os.path.join(safe_makedir(out_dir), "sample_file.txt")
_write_sample_id_file(data, bam_file, sample_file)
runner = rnaseqc_runner_from_config(config)
bam.index(bam_file, config)
single_end = bam.is_paired(bam_file)
runner.run(sample_file, ref_file, rna_file, gtf_file, out_dir,
single_end)
return _parse_rnaseqc_metrics(metrics_file, data["name"][-1])
def sample_summary(bam_file, data, out_dir):
"""Run RNA-SeQC on a single RNAseq sample, writing to specified output directory.
"""
metrics_file = os.path.join(out_dir, "metrics.tsv")
if not file_exists(metrics_file):
with file_transaction(out_dir) as tx_out_dir:
config = data["config"]
ref_file = data["sam_ref"]
genome_dir = os.path.dirname(os.path.dirname(ref_file))
gtf_file = config_utils.get_transcript_gtf(genome_dir)
rna_file = config_utils.get_rRNA_sequence(genome_dir)
sample_file = os.path.join(safe_makedir(tx_out_dir), "sample_file.txt")
_write_sample_id_file(data, bam_file, sample_file)
runner = rnaseqc_runner_from_config(config)
bam.index(bam_file, config)
single_end = not bam.is_paired(bam_file)
runner.run(sample_file, ref_file, rna_file, gtf_file, tx_out_dir, single_end)
# we don't need this large directory for just the report
shutil.rmtree(os.path.join(tx_out_dir, data["description"]))
return _parse_rnaseqc_metrics(metrics_file, data["name"][-1])
def make_refflat(genome_dir):
"""
makes a refflat file for use with Picard from a GTF file
"""
gtf_file = get_transcript_gtf(genome_dir)
base, _ = os.path.splitext(gtf_file)
refflat_file = base + ".refFlat"
print "Making %s into a refFlat file named %s." % (gtf_file, refflat_file)
if file_exists(refflat_file):
print "%s already exists, skipping." % refflat_file
return refflat_file
with tmpfile(dir=os.getcwd(), prefix="genepred") as tmp_file:
cmd = "gtfToGenePred {gtf_file} {tmp_file}".format(**locals())
subprocess.check_call(cmd, shell=True)
with open(tmp_file) as tmp_handle, open(refflat_file, "w") as out_handle:
for line in tmp_handle:
l = line.split("\t")
l = [l[0]] + l
out_handle.write("\t".join(l) + "\n")
return refflat_file
def make_refflat(genome_dir):
"""
makes a refflat file for use with Picard from a GTF file
"""
gtf_file = get_transcript_gtf(genome_dir)
base, _ = os.path.splitext(gtf_file)
refflat_file = base + ".refFlat"
print "Making %s into a refFlat file named %s." % (gtf_file, refflat_file)
if file_exists(refflat_file):
print "%s already exists, skipping." % refflat_file
return refflat_file
with tmpfile(dir=os.getcwd(), prefix="genepred") as tmp_file:
cmd = "gtfToGenePred {gtf_file} {tmp_file}".format(**locals())
subprocess.check_call(cmd, shell=True)
with open(tmp_file) as tmp_handle, open(refflat_file,
"w") as out_handle:
for line in tmp_handle:
l = line.split("\t")
l = [l[0]] + l
out_handle.write("\t".join(l) + "\n")
return refflat_file
def sample_summary(bam_file, data, out_dir):
"""Run RNA-SeQC on a single RNAseq sample, writing to specified output directory.
"""
metrics_file = os.path.join(out_dir, "metrics.tsv")
if not file_exists(metrics_file):
with file_transaction(out_dir) as tx_out_dir:
config = data["config"]
ref_file = data["sam_ref"]
genome_dir = os.path.dirname(os.path.dirname(ref_file))
gtf_file = config_utils.get_transcript_gtf(genome_dir)
rna_file = config_utils.get_rRNA_sequence(genome_dir)
sample_file = os.path.join(safe_makedir(tx_out_dir),
"sample_file.txt")
_write_sample_id_file(data, bam_file, sample_file)
runner = rnaseqc_runner_from_config(config)
bam.index(bam_file, config)
single_end = not bam.is_paired(bam_file)
runner.run(sample_file, ref_file, rna_file, gtf_file, tx_out_dir,
single_end)
# we don't need this large directory for just the report
shutil.rmtree(os.path.join(tx_out_dir, data["description"]))
return _parse_rnaseqc_metrics(metrics_file, data["name"][-1])
