def run_bam_to_bam(subread_set_file, barcode_set_file, output_file_name,
nproc=1, score_mode="symmetric"):
if not score_mode in ["asymmetric", "symmetric"]:
raise ValueError("Unrecognized score mode '{m}'".format(m=score_mode))
bc = BarcodeSet(barcode_set_file)
if len(bc.resourceReaders()) > 1:
raise NotImplementedError("Multi-FASTA BarcodeSet input is not supported.")
new_prefix = re.sub(".subreadset.xml$", "", output_file_name)
args = [
"bam2bam",
"-j", str(nproc),
"-b", str(nproc),
"-o", new_prefix,
"--barcodes", barcode_set_file,
"--scoreMode", score_mode,
subread_set_file
]
log.info(" ".join(args))
result = run_cmd(" ".join(args),
stdout_fh=sys.stdout,
stderr_fh=sys.stderr)
if result.exit_code != 0:
return result.exit_code
assert op.isfile(output_file_name)
tmp_out = op.join(op.dirname(output_file_name),
"tmp_" + op.basename(output_file_name))
shutil.move(output_file_name, tmp_out)
with SubreadSet(tmp_out, strict=True) as ds:
with SubreadSet(subread_set_file) as ds_in:
ds.metadata = ds_in.metadata
ds.name = ds_in.name + " (barcoded)"
ds.updateCounts()
ds.newUuid()
ds.write(output_file_name)
return 0
def run_bam_to_bam(subread_set_file, barcode_set_file, output_file_name,
nproc=1, score_mode="symmetric"):
if not score_mode in ["asymmetric", "symmetric"]:
raise ValueError("Unrecognized score mode '{m}'".format(m=score_mode))
bc = BarcodeSet(barcode_set_file)
if len(bc.resourceReaders()) > 1:
raise NotImplementedError("Multi-FASTA BarcodeSet input is not supported.")
new_prefix = re.sub(".subreadset.xml$", "", output_file_name)
args = [
"bam2bam",
"-j", str(nproc),
"-b", str(nproc),
"-o", new_prefix,
"--barcodes", barcode_set_file,
"--scoreMode", score_mode,
subread_set_file
]
log.info(" ".join(args))
result = run_cmd(" ".join(args),
stdout_fh=sys.stdout,
stderr_fh=sys.stderr)
if result.exit_code != 0:
return result.exit_code
assert op.isfile(output_file_name)
tmp_out = op.join(op.dirname(output_file_name),
"tmp_" + op.basename(output_file_name))
shutil.move(output_file_name, tmp_out)
with SubreadSet(tmp_out, strict=True) as ds:
with SubreadSet(subread_set_file) as ds_in:
ds.metadata = ds_in.metadata
ds.name = ds_in.name + " (barcoded)"
ds.updateCounts()
ds.newUuid()
ds.write(output_file_name)
return 0
def run_bam_to_bam(subread_set_file, barcode_set_file, output_file_name,
nproc=1):
bc = BarcodeSet(barcode_set_file)
if len(bc.resourceReaders()) > 1:
raise NotImplementedError("Multi-FASTA BarcodeSet input is not supported.")
barcode_fasta = bc.toExternalFiles()[0]
with SubreadSet(subread_set_file) as ds:
# TODO(nechols)(2016-03-15): replace with BarcodedSubreadSet
ds_new = SubreadSet(strict=True)
for ext_res in ds.externalResources:
subreads_bam = ext_res.bam
scraps_bam = ext_res.scraps
assert subreads_bam is not None
if scraps_bam is None:
raise TypeError("The input SubreadSet must include scraps.")
new_prefix = op.join(op.dirname(output_file_name),
re.sub(".subreads.bam", "_barcoded", op.basename(subreads_bam)))
if not op.isabs(subreads_bam):
subreads_bam = op.join(op.dirname(subread_set_file),
subreads_bam)
if not op.isabs(scraps_bam):
scraps_bam = op.join(op.dirname(subread_set_file), scraps_bam)
args = [
"bam2bam",
"-j", str(nproc),
"-b", str(nproc),
"-o", new_prefix,
"--barcodes", barcode_fasta,
subreads_bam, scraps_bam
]
print args
log.info(" ".join(args))
result = run_cmd(" ".join(args),
stdout_fh=sys.stdout,
stderr_fh=sys.stderr)
if result.exit_code != 0:
return result.exit_code
subreads_bam = new_prefix + ".subreads.bam"
scraps_bam = new_prefix + ".scraps.bam"
assert op.isfile(subreads_bam), "Missing {f}".format(f=subreads_bam)
# FIXME we need a more general method for this
ext_res_new = ExternalResource()
ext_res_new.resourceId = subreads_bam
ext_res_new.metaType = 'PacBio.SubreadFile.SubreadBamFile'
ext_res_new.addIndices([subreads_bam + ".pbi"])
ext_res_inner = ExternalResources()
ext_res_scraps = ExternalResource()
ext_res_scraps.resourceId = scraps_bam
ext_res_scraps.metaType = 'PacBio.SubreadFile.ScrapsBamFile'
ext_res_scraps.addIndices([scraps_bam + ".pbi"])
ext_res_inner.append(ext_res_scraps)
ext_res_new.append(ext_res_inner)
ds_new.externalResources.append(ext_res_new)
ds._filters.clearCallbacks()
ds_new._filters = ds._filters
ds_new._populateMetaTypes()
ds_new.updateCounts()
ds_new.write(output_file_name)
return 0
def run_bam_to_bam(subread_set_file,
barcode_set_file,
output_file_name,
nproc=1,
score_mode="symmetric"):
if not score_mode in ["asymmetric", "symmetric"]:
raise ValueError("Unrecognized score mode '{m}'".format(m=score_mode))
bc = BarcodeSet(barcode_set_file)
if len(bc.resourceReaders()) > 1:
raise NotImplementedError(
"Multi-FASTA BarcodeSet input is not supported.")
barcode_fasta = bc.toExternalFiles()[0]
with SubreadSet(subread_set_file) as ds:
ds_new = SubreadSet(strict=True)
for ext_res in ds.externalResources:
subreads_bam = ext_res.bam
scraps_bam = ext_res.scraps
assert subreads_bam is not None
if scraps_bam is None:
raise TypeError("The input SubreadSet must include scraps.")
new_prefix = op.join(
op.dirname(output_file_name),
re.sub(".subreads.bam", "_barcoded",
op.basename(subreads_bam)))
if not op.isabs(subreads_bam):
subreads_bam = op.join(op.dirname(subread_set_file),
subreads_bam)
if not op.isabs(scraps_bam):
scraps_bam = op.join(op.dirname(subread_set_file), scraps_bam)
args = [
"bam2bam", "-j",
str(nproc), "-b",
str(nproc), "-o", new_prefix, "--barcodes", barcode_fasta,
"--scoreMode", score_mode, subreads_bam, scraps_bam
]
log.info(" ".join(args))
result = run_cmd(" ".join(args),
stdout_fh=sys.stdout,
stderr_fh=sys.stderr)
if result.exit_code != 0:
return result.exit_code
subreads_bam = new_prefix + ".subreads.bam"
scraps_bam = new_prefix + ".scraps.bam"
assert op.isfile(subreads_bam), "Missing {f}".format(
f=subreads_bam)
add_subread_resources(ds_new,
subreads=subreads_bam,
scraps=scraps_bam,
barcodes=barcode_set_file)
ds._filters.clearCallbacks()
ds_new._filters = ds._filters
ds_new._populateMetaTypes()
ds_new.metadata = ds.metadata
ds_new.name = ds.name + " (barcoded)"
ds_new.updateCounts()
ds_new.newUuid()
ds_new.write(output_file_name)
return 0
def run_bam_to_bam(subread_set_file, barcode_set_file, output_file_name,
nproc=1, score_mode="symmetric"):
if not score_mode in ["asymmetric", "symmetric"]:
raise ValueError("Unrecognized score mode '{m}'".format(m=score_mode))
bc = BarcodeSet(barcode_set_file)
if len(bc.resourceReaders()) > 1:
raise NotImplementedError("Multi-FASTA BarcodeSet input is not supported.")
barcode_fasta = bc.toExternalFiles()[0]
with SubreadSet(subread_set_file) as ds:
ds_new = SubreadSet(strict=True)
for ext_res in ds.externalResources:
subreads_bam = ext_res.bam
scraps_bam = ext_res.scraps
assert subreads_bam is not None
if scraps_bam is None:
raise TypeError("The input SubreadSet must include scraps.")
new_prefix = op.join(op.dirname(output_file_name),
re.sub(".subreads.bam", "_barcoded", op.basename(subreads_bam)))
if not op.isabs(subreads_bam):
subreads_bam = op.join(op.dirname(subread_set_file),
subreads_bam)
if not op.isabs(scraps_bam):
scraps_bam = op.join(op.dirname(subread_set_file), scraps_bam)
args = [
"bam2bam",
"-j", str(nproc),
"-b", str(nproc),
"-o", new_prefix,
"--barcodes", barcode_fasta,
"--scoreMode", score_mode,
subreads_bam, scraps_bam
]
log.info(" ".join(args))
result = run_cmd(" ".join(args),
stdout_fh=sys.stdout,
stderr_fh=sys.stderr)
if result.exit_code != 0:
return result.exit_code
subreads_bam = new_prefix + ".subreads.bam"
scraps_bam = new_prefix + ".scraps.bam"
assert op.isfile(subreads_bam), "Missing {f}".format(f=subreads_bam)
add_subread_resources(ds_new,
subreads=subreads_bam,
scraps=scraps_bam,
barcodes=barcode_set_file)
ds._filters.clearCallbacks()
ds_new._filters = ds._filters
ds_new._populateMetaTypes()
ds_new.metadata = ds.metadata
ds_new.name = ds.name + " (barcoded)"
ds_new.updateCounts()
ds_new.newUuid()
ds_new.write(output_file_name)
return 0
