def run(items, config):
"""Run third party disambiguation script, resolving into single set of calls.
"""
assert len(items) == 2, "Can only resolve two organism disambiguation"
# check aligner, handling tophat/tophat2 distinctions
aligner = config["algorithm"].get("aligner")
aligner = "tophat" if aligner.startswith("tophat") else aligner
assert aligner in ["bwa", "tophat", "star"], "Disambiguation only supported for bwa, star and tophat alignments."
if items[0]["disambiguate"].get("base"):
data_a, data_b = items
else:
data_b, data_a = items
work_bam_a = bam.sort(data_a["work_bam"], config, "queryname")
work_bam_b = bam.sort(data_b["work_bam"], config, "queryname")
out_dir = os.path.normpath(os.path.join(os.path.dirname(work_bam_a),
os.pardir, "disambiguate_%s" % aligner))
base_name = os.path.join(out_dir, os.path.splitext(os.path.basename(work_bam_a))[0])
summary_file = "%s_summary.txt" % base_name
if not utils.file_exists(summary_file):
with file_transaction(items[0], out_dir) as tx_out_dir:
Args = collections.namedtuple("Args", "A B output_dir intermediate_dir "
"no_sort prefix aligner")
args = Args(work_bam_a, work_bam_b, tx_out_dir, tx_out_dir,
True, "", aligner)
disambiguate_main(args)
data_a["disambiguate"] = \
{data_b["genome_build"]: "%s.disambiguatedSpeciesB.bam" % base_name,
"%s-ambiguous" % data_a["genome_build"]: "%s.ambiguousSpeciesA.bam" % base_name,
"%s-ambiguous" % data_b["genome_build"]: "%s.ambiguousSpeciesB.bam" % base_name,
"summary": summary_file}
data_a["work_bam"] = bam.sort("%s.disambiguatedSpeciesA.bam" % base_name, config)
return [[data_a]]
def _run_python(work_bam_a, work_bam_b, out_dir, aligner, prefix, items):
"""Run python version of disambiguation
"""
Args = collections.namedtuple("Args", "A B output_dir intermediate_dir "
"no_sort prefix aligner")
args = Args(work_bam_a, work_bam_b, out_dir, out_dir, True, "", aligner)
disambiguate_main(args)
def _run_python(work_bam_a, work_bam_b, out_dir, aligner, prefix, items):
"""Run python version of disambiguation
"""
Args = collections.namedtuple("Args", "A B output_dir intermediate_dir "
"no_sort prefix aligner")
args = Args(work_bam_a, work_bam_b, out_dir, out_dir, True, "", aligner)
disambiguate_main(args)
def run(items, config):
"""Run third party disambiguation script, resolving into single set of calls.
"""
assert len(items) == 2, "Can only resolve two organism disambiguation"
# check aligner, handling tophat/tophat2 distinctions
aligner = config["algorithm"].get("aligner")
aligner = "tophat" if aligner.startswith("tophat") else aligner
assert aligner in [
"bwa", "hisat2", "tophat", "star"
], "Disambiguation only supported for bwa, hisat2, star and tophat alignments."
if items[0]["disambiguate"].get("base"):
data_a, data_b = items
else:
data_b, data_a = items
work_bam_a = bam.sort(data_a["work_bam"], config, "queryname")
work_bam_b = bam.sort(data_b["work_bam"], config, "queryname")
if data_a.get("align_split"):
base_dir = utils.safe_makedir(
os.path.normpath(
os.path.join(os.path.dirname(work_bam_a), os.pardir, os.pardir,
"disambiguate_%s" % aligner)))
out_dir = os.path.join(
base_dir,
"_".join([str(x) for x in data_a["align_split"].split("-")]))
else:
out_dir = os.path.normpath(
os.path.join(os.path.dirname(work_bam_a), os.pardir,
"disambiguate_%s" % aligner))
base_name = os.path.join(out_dir,
os.path.splitext(os.path.basename(work_bam_a))[0])
summary_file = "%s_summary.txt" % base_name
if not utils.file_exists(summary_file):
with file_transaction(items[0], out_dir) as tx_out_dir:
Args = collections.namedtuple(
"Args", "A B output_dir intermediate_dir "
"no_sort prefix aligner")
args = Args(work_bam_a, work_bam_b, tx_out_dir, tx_out_dir, True,
"", aligner)
disambiguate_main(args)
data_a["disambiguate"] = \
{data_b["genome_build"]: bam.sort("%s.disambiguatedSpeciesB.bam" % base_name, config),
"%s-ambiguous" % data_a["genome_build"]: bam.sort("%s.ambiguousSpeciesA.bam" % base_name, config),
"%s-ambiguous" % data_b["genome_build"]: bam.sort("%s.ambiguousSpeciesB.bam" % base_name, config),
"summary": summary_file}
data_a["work_bam"] = bam.sort("%s.disambiguatedSpeciesA.bam" % base_name,
config)
return [[data_a]]