本文整理汇总了Python中pbcore.io.SubreadSet.name方法的典型用法代码示例。如果您正苦于以下问题：Python SubreadSet.name方法的具体用法？Python SubreadSet.name怎么用？Python SubreadSet.name使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pbcore.io.SubreadSet的用法示例。
在下文中一共展示了SubreadSet.name方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: run_bax_to_bam
# 需要导入模块: from pbcore.io import SubreadSet [as 别名]
# 或者: from pbcore.io.SubreadSet import name [as 别名]
def run_bax_to_bam(input_file_name, output_file_name):
with HdfSubreadSet(input_file_name) as ds_in:
movies = set()
for rr in ds_in.resourceReaders():
movies.add(rr.movieName)
if len(movies) > 1:
out_dir = os.path.dirname(output_file_name)
ds_out_files = []
for bax_file in ds_in.toExternalFiles():
output_file_name_tmp = os.path.join(out_dir, ".".join(
os.path.basename(bax_file).split(".")[:-2]) +
".hdfsubreadset.xml")
rc = _run_bax_to_bam(bax_file, output_file_name_tmp)
if rc != 0:
log.error("bax2bam failed")
return rc
ds_out_files.append(output_file_name_tmp)
ds = SubreadSet(*ds_out_files)
ds.name = ds_in.name
if 'Description' in ds_in.objMetadata:
ds.objMetadata['Description'] = ds_in.objMetadata['Description']
ds.metadata.merge(ds_in.metadata)
ds.write(output_file_name)
else:
return _run_bax_to_bam(input_file_name, output_file_name)
return 0示例2: run_bam_to_bam
# 需要导入模块: from pbcore.io import SubreadSet [as 别名]
# 或者: from pbcore.io.SubreadSet import name [as 别名]
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