def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("dataset_xml", help="Path to input dataset")
p.add_argument("output_file", help="Name of output dataset file")
p.add_argument("--biosample-name", default=None, help="New BioSample Name")
p.add_argument("--library-name", default=None, help="New Library Name")
return p
def get_parser_impl(constants):
fmt_name = constants.FORMAT_NAME
p = get_base_parser(constants.DESC)
p.add_argument("bam", help="Input PacBio dataset XML or BAM file")
p.add_argument(
"{f}_out".format(f=fmt_name),
help="Exported {f} as ZIP archive".format(f=fmt_name.upper()))
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("datastore_in",
help="DataStore JSON of ConsensusReadSet files")
p.add_argument("datastore_out", help="DataStore JSON of FASTQ files")
p.add_argument("--nproc", type=int, default=1,
help="Number of processors to use")
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("ccsxml", help="Path to input dataset")
p.add_argument("--zmws-json",
action="store",
default=None,
help="Path to zmws.json.gz")
p.add_argument("--report-ccs-processing",
action="store",
default=None,
help="Path to ccs_processing.report.json")
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("barcodes", help="BarcodeSet XML or FASTA")
p.add_argument("dataset",
help="Reads (Subreads or CCS) PacBio dataset XML")
p.add_argument("--symmetric",
action="store_true",
dest="symmetric_barcodes",
default=None,
help="Symmetric barcode pairs")
p.add_argument("--asymmetric",
action="store_false",
dest="symmetric_barcodes",
help="Asymmetric barcode pairs")
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("flnc_ccs", help="Full-Length Non-Chimeric CCS Reads")
p.add_argument("--cluster-csv", default=None, help="Cluster Report CSV")
p.add_argument("--transcripts-hq", default=None, help="HQ TranscriptSet")
p.add_argument("--transcripts-lq", default=None, help="LQ TranscriptSet")
p.add_argument("--collapse-fasta", default=None, help="Collapsed Isoforms")
#p.add_argument("--collapse-gff", default=None, help="Collapsed Isoform GFF")
p.add_argument("--read-stats",
default=None,
help="Collapsed Isoform Read Info")
p.add_argument("--datastore-prefix",
default="sample",
help="Prefix for output per-sample datastore.json files")
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("dataset", help="PacBio dataset XML")
p.add_argument("--skip-counts",
action="store_true",
default=True,
help="Don't load database indices")
p.add_argument("--no-skip-counts",
action="store_false",
dest="skip_counts",
help="Load database indices and recalculate size")
p.add_argument("--get-index-size",
action="store_true",
help="Compute file index size")
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("samples_file", help="BAM file with sample name")
for file_id, _, label in FILE_IDS_AND_NAMES:
p.add_argument("--{}".format(file_id.replace("_", "-")),
default=None,
help=label)
p.add_argument("--single-sample",
action="store_true",
default=False,
help="Indicates whether the analysis has only one sample")
p.add_argument(
"--all-samples",
action="store_true",
default=False,
help=
"Indicates whether the outputs are for all samples in a multi-sample experiment"
)
p.add_argument("--datastore",
default="isoseq_sample.datastore.json",
help="Output JSON file name")
return p
def get_parser():
"""
Input:
idx - 0 SubreadSet
idx - 1 HQ TranscriptSet
idx - 2 LQ TranscriptSet
Output:
idx - 0 HQ TranscriptSet, of which read names have biosample_HQ prefix
idx - 1 LQ TranscriptSet, of which read names have biosample_LQ prefix
idx - 2 HQ DataStore of output TranscriptSet BAM file
idx - 3 LQ DataStore of output TranscriptSet BAM file
"""
p = get_base_parser(__doc__)
p.add_argument("subreads", help="SubreadSet with biosample metadata.")
p.add_argument("hq_ds_in", help="Gathered HQ transcripts")
p.add_argument("lq_ds_in", help="Gathered LQ transcripts")
p.add_argument("hq_ds_out", help="Output HQ transcripts")
p.add_argument("lq_ds_out", help="Output LQ transcripts")
p.add_argument("hq_datastore",
help="Datastore containing HQ transcripts BAM")
p.add_argument("lq_datastore",
help="Datastore containing LQ transcripts BAM")
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("barcodeset", help="BarcodeSet XML")
return p
def get_parser():
p = get_base_parser(__doc__)
p.add_argument("subreads", help="Input SubreadSet XML")
p.add_argument("fastq_out", help="Exported FASTQ")
return p
def get_parser():
parser = get_base_parser(__doc__, log_level="CRITICAL")
parser.add_argument('file', help="BAM, FASTA, or DataSet XML file")
parser.add_argument("--quick",
dest="quick",
action="store_true",
help="Limits validation to the first 100 records " +
"(plus file header); equivalent to " +
"--max-records=100")
parser.add_argument("--max",
dest="max_errors",
action="store",
type=int,
help="Exit after MAX_ERRORS have been recorded " +
"(DEFAULT: check entire file)")
parser.add_argument("--max-records",
dest="max_records",
action="store",
type=int,
help="Exit after MAX_RECORDS have been inspected " +
"(DEFAULT: check entire file)")
parser.add_argument("--type",
dest="file_type",
action="store",
choices=["BAM", "Fasta"] + dataset.DatasetTypes.ALL,
help="Use the specified file type instead of guessing")
parser.add_argument(
"--index",
dest="validate_index",
action="store_true",
help=
"Require index files (.fai or .pbi); this is always enforced for dataset XML"
)
parser.add_argument("--strict",
dest="strict",
action="store_true",
help="Turn on additional validation, primarily for " +
"DataSet XML")
parser.add_argument(
"--instrument",
dest="instrument_mode",
action="store_true",
help=
"Indicates that the dataset is delivered from a PacBio instrument and should be checked for metadata consistency"
)
parser.add_argument("-x",
"--xunit-out",
dest="xunit_out",
action="store",
default=None,
help="Xunit test results for Jenkins")
parser.add_argument("--alarms",
dest="alarms_out",
action="store",
default=None,
help="alarms.json for errors")
g1 = parser.add_argument_group('bam', "BAM options")
g2 = parser.add_argument_group('fasta', "Fasta options")
bam.get_format_specific_args(g1)
fasta.get_format_specific_args(g2)
return parser
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("datasets", nargs="+", help="Paths to chunked datasets")
return p
def _get_parser():
p = get_base_parser(__doc__)
p.add_argument("datastore", help="Datastore of trimmed reads")
p.add_argument("ccs_in", help="Input (untrimmed) CCS reads")
return p