def singlecell_rnaseq(samples, run_parallel):
quantifier = dd.get_in_samples(samples, dd.get_singlecell_quantifier)
quantifier = quantifier.lower()
samples = run_parallel("run_umi_transform", samples)
demultiplexed = run_parallel("demultiplex_samples", samples)
# break demultiplixed lanes into their own samples
samples = []
for lane in demultiplexed:
for index in lane:
samples.append([index])
samples = run_parallel("run_filter_barcodes", samples)
samples = run_parallel("run_barcode_histogram", samples)
if quantifier == "rapmap":
samples = run_parallel("run_rapmap_index", [samples])
samples = run_parallel("run_rapmap_align", samples)
samples = run_parallel("run_tagcount", samples)
samples = run_parallel("run_concatenate_sparse_counts", [samples])
elif quantifier == "kallisto":
samples = run_parallel("run_kallisto_singlecell", samples)
else:
logger.error(("%s is not supported for singlecell RNA-seq "
"quantification." % quantifier))
sys.exit(1)
samples = scrnaseq_concatenate_metadata(samples)
singlecellexperiment.make_scrnaseq_object(samples)
return samples
def singlecell_rnaseq(samples, run_parallel):
quantifier = dd.get_in_samples(samples, dd.get_singlecell_quantifier)
quantifier = quantifier.lower()
samples = run_parallel("run_umi_transform", samples)
demultiplexed = run_parallel("demultiplex_samples", samples)
# break demultiplixed lanes into their own samples
samples = []
for lane in demultiplexed:
for index in lane:
samples.append([index])
samples = run_parallel("run_filter_barcodes", samples)
samples = run_parallel("run_barcode_histogram", samples)
if quantifier == "rapmap":
samples = run_parallel("run_rapmap_index", [samples])
samples = run_parallel("run_rapmap_align", samples)
samples = run_parallel("run_tagcount", samples)
samples = run_parallel("run_concatenate_sparse_counts", [samples])
elif quantifier == "kallisto":
samples = run_parallel("run_kallisto_singlecell", samples)
else:
logger.error(("%s is not supported for singlecell RNA-seq "
"quantification." % quantifier))
sys.exit(1)
samples = scrnaseq_concatenate_metadata(samples)
singlecellexperiment.make_scrnaseq_object(samples)
return samples
def singlecell_rnaseq(samples, run_parallel):
quantifier = dd.get_in_samples(samples, dd.get_singlecell_quantifier)
quantifier = quantifier.lower()
samples = run_parallel("run_umi_transform", samples)
demultiplexed = run_parallel("demultiplex_samples", samples)
# break demultiplixed lanes into their own samples
samples = []
for lane in demultiplexed:
for index in lane:
samples.append([index])
if not samples:
logger.error(f"No samples were found matching the supplied sample barcodes. See "
f"https://github.com/bcbio/bcbio-nextgen/issues/3428#issuecomment-772609904 "
f"for how to debug this issue.")
sys.exit(1)
samples = run_parallel("run_filter_barcodes", samples)
samples = run_parallel("run_barcode_histogram", samples)
if quantifier == "rapmap":
samples = run_parallel("run_rapmap_index", [samples])
samples = run_parallel("run_rapmap_align", samples)
samples = run_parallel("run_tagcount", samples)
samples = run_parallel("run_concatenate_sparse_counts", [samples])
elif quantifier == "kallisto":
samples = run_parallel("run_kallisto_singlecell", samples)
else:
logger.error(("%s is not supported for singlecell RNA-seq "
"quantification." % quantifier))
sys.exit(1)
samples = scrnaseq_concatenate_metadata(samples)
singlecellexperiment.make_scrnaseq_object(samples)
return samples