def test_htseq_count(self):
data = {"work_bam": self.in_bam,
"sam_ref": os.path.join(self.data_dir, "foo"),
"dirs": {"work": self.out_dir},
"config": {"algorithm": {"transcripts": self.in_gtf}}}
out_file = count.htseq_count(data)
self.assertTrue(file_exists(out_file))
def test_htseq_count(self):
data = {"work_bam": self.in_bam,
"sam_ref": os.path.join(self.data_dir, "foo"),
"dirs": {"work": self.out_dir},
"config": {"algorithm": {"transcripts": self.in_gtf}}}
out_file = count.htseq_count(data)
self.assertTrue(file_exists(out_file))
def count(data):
"""
count reads mapping to genes using featureCounts
falls back on htseq_count method if featureCounts is not
found
"""
in_bam = dd.get_work_bam(data)
gtf_file = dd.get_gtf_file(data)
work_dir = dd.get_work_dir(data)
out_dir = os.path.join(work_dir, "htseq-count")
safe_makedir(out_dir)
count_file = os.path.join(out_dir, dd.get_sample_name(data)) + ".counts"
if file_exists(count_file):
return count_file
config = data["config"]
try:
featureCounts = config_utils.get_program("featureCounts", config)
except config_utils.CmdNotFound:
logger.info(
"featureCounts not found, falling back to htseq-count "
"for feature counting. You can upgrade the tools to "
"install featureCount with bcbio_nextgen.py upgrade "
"--tools."
)
return htseq_count(data)
paired_flag = _paired_flag(in_bam)
strand_flag = _strand_flag(config)
cmd = "{featureCounts} -a {gtf_file} -o {tx_count_file} -s {strand_flag} " "{paired_flag} {in_bam}"
message = "Count reads in {tx_count_file} mapping to {gtf_file} using " "featureCounts"
with file_transaction(count_file) as tx_count_file:
do.run(cmd.format(**locals()), message.format(**locals()))
fixed_count_file = _format_count_file(count_file)
os.rename(fixed_count_file, count_file)
return count_file
def count(data):
"""
count reads mapping to genes using featureCounts
falls back on htseq_count method if featureCounts is not
found
"""
in_bam = data["work_bam"]
gtf_file = data["genome_resources"]["rnaseq"]["transcripts"]
work_dir = data["dirs"].get("work", "work")
out_dir = os.path.join(work_dir, "htseq-count")
safe_makedir(out_dir)
count_file = _count_file_name(in_bam, out_dir)
if file_exists(count_file):
return count_file
config = data["config"]
try:
featureCounts = config_utils.get_program("featureCounts", config)
except config_utils.CmdNotFound:
logger.info("featureCounts not found, falling back to htseq-count "
"for feature counting. You can upgrade the tools to "
"install featureCount with bcbio_nextgen.py upgrade "
"--tools.")
return htseq_count(data)
paired_flag = _paired_flag(in_bam)
strand_flag = _strand_flag(config)
cmd = ("{featureCounts} -a {gtf_file} -o {tx_count_file} -s {strand_flag} "
"{paired_flag} {in_bam}")
message = ("Count reads in {tx_count_file} mapping to {gtf_file} using "
"featureCounts")
with file_transaction(count_file) as tx_count_file:
do.run(cmd.format(**locals()), message.format(**locals()))
fixed_count_file = _format_count_file(count_file)
os.rename(fixed_count_file, count_file)
return count_file
def generate_transcript_counts(data):
"""Generate counts per transcript from an alignment"""
data["count_file"] = count.htseq_count(data)
return [[data]]
def generate_transcript_counts(data):
"""Generate counts per transcript from an alignment"""
data["count_file"] = count.htseq_count(data)
if get_in(data, ("config", "algorithm", "fusion_mode"), False):
data["oncofuse_file"] = oncofuse.run(data)
return [[data]]