def quantitate(data):
"""CWL target for quantitation.
XXX Needs to be split and parallelized by expression caller, with merging
of multiple calls.
"""
data = to_single_data(to_single_data(data))
data = generate_transcript_counts(data)[0][0]
data["quant"] = {}
if "sailfish" in dd.get_expression_caller(data):
data = to_single_data(sailfish.run_sailfish(data)[0])
data["quant"]["tsv"] = data["sailfish"]
data["quant"]["hdf5"] = os.path.join(os.path.dirname(data["sailfish"]),
"abundance.h5")
if ("kallisto" in dd.get_expression_caller(data)
or "pizzly" in dd.get_fusion_caller(data, [])):
data = to_single_data(kallisto.run_kallisto_rnaseq(data)[0])
data["quant"]["tsv"] = os.path.join(data["kallisto_quant"],
"abundance.tsv")
data["quant"]["hdf5"] = os.path.join(data["kallisto_quant"],
"abundance.h5")
if (os.path.exists(os.path.join(data["kallisto_quant"], "fusion.txt"))):
data["quant"]["fusion"] = os.path.join(data["kallisto_quant"],
"fusion.txt")
else:
data["quant"]["fusion"] = None
if "salmon" in dd.get_expression_caller(data):
if dd.get_quantify_genome_alignments(data):
if dd.get_aligner(data).lower() != "star":
if dd.get_genome_build(data) == "hg38":
logger.warning(
"Whole genome alignment-based Salmon quantification is "
"only supported for the STAR aligner. Since this is hg38 we will fall "
"back to the decoy method")
data = to_single_data(salmon.run_salmon_decoy(data)[0])
else:
logger.warning(
"Whole genome alignment-based Salmon quantification is "
"only supported for the STAR aligner. Falling back to the "
"transcriptome-only method.")
data = to_single_data(salmon.run_salmon_reads(data)[0])
else:
data = to_single_data(salmon.run_salmon_bam(data)[0])
else:
data = to_single_data(salmon.run_salmon_reads(data)[0])
data["quant"]["tsv"] = data["salmon"]
data["quant"]["hdf5"] = os.path.join(os.path.dirname(data["salmon"]),
"abundance.h5")
return [[data]]
def quantitate_expression_parallel(samples, run_parallel):
"""
quantitate expression, all programs run here should be multithreaded to
take advantage of the threaded run_parallel environment
"""
data = samples[0][0]
to_index = determine_indexes_to_make(samples)
samples = run_parallel("generate_transcript_counts", samples)
if "cufflinks" in dd.get_expression_caller(data):
samples = run_parallel("run_cufflinks", samples)
if "stringtie" in dd.get_expression_caller(data):
samples = run_parallel("run_stringtie_expression", samples)
if ("kallisto" in dd.get_expression_caller(data)
or dd.get_fusion_mode(data)
or "pizzly" in dd.get_fusion_caller(data, [])):
run_parallel("run_kallisto_index", [to_index])
samples = run_parallel("run_kallisto_rnaseq", samples)
if "sailfish" in dd.get_expression_caller(data):
run_parallel("run_sailfish_index", [to_index])
samples = run_parallel("run_sailfish", samples)
# always run salmon
run_parallel("run_salmon_index", [to_index])
if dd.get_quantify_genome_alignments(data):
if dd.get_aligner(data).lower() != "star":
if dd.get_genome_build(data) == "hg38":
logger.warning(
"Whole genome alignment-based Salmon quantification is "
"only supported for the STAR aligner. Since this is hg38 we will fall "
"back to the decoy method")
samples = run_parallel("run_salmon_decoy", samples)
else:
logger.warning(
"Whole genome alignment-based Salmon quantification is "
"only supported for the STAR aligner. Falling back to the "
"transcriptome-only method.")
samples = run_parallel("run_salmon_reads", samples)
else:
samples = run_parallel("run_salmon_bam", samples)
else:
samples = run_parallel("run_salmon_reads", samples)
samples = run_parallel("detect_fusions", samples)
return samples