def get_parser():
parser = get_default_argparser_with_base_opts(
version=__version__,
description=__doc__,
default_level="CRITICAL")
parser.add_argument('file', help="BAM, FASTA, or DataSet XML file")
parser.add_argument("-c", dest="use_termcolor", action="store_true")
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)")
parser.add_argument("--strict", dest="strict", action="store_true",
help="Turn on additional validation, primarily for "+
"DataSet XML")
parser.add_argument("-x", "--xunit-out", dest="xunit_out", action="store",
default=None, help="Xunit test results for Jenkins")
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_default_argparser_with_base_opts(
version=VERSION,
description=__doc__,
default_level="WARN")
p.add_argument("input_bam",
help="Input BAM or DataSet from which reads will be read")
p.add_argument("output_bam", nargs='?', default=None,
help="Output BAM or DataSet to which filtered reads will "
"be written")
p.add_argument("--show-zmws", action="store_true", default=False,
help="Print a list of ZMWs and exit")
p.add_argument("--whitelist", action="store", default=None,
help="Comma-separated list of ZMWs, or file containing " +
"whitelist of one hole number per line, or " +
"BAM/DataSet file from which to extract ZMWs")
p.add_argument("--blacklist", action="store", default=None,
help="Opposite of --whitelist, specifies ZMWs to discard")
p.add_argument("--percentage", action="store", type=float, default=None,
help="If you prefer to recover a percentage of a SMRTcell "
"rather than a specific list of reads specify that "
"percentage (range 0-100) here")
p.add_argument("-n", "--count", action="store", type=int, default=None,
help="Recover a specific number of ZMWs picked at random")
p.add_argument("-s", "--seed", action="store", type=int, default=None,
help="Random seed for selecting a percentage of reads")
p.add_argument("--ignore-metadata", action="store_true",
help="Discard input DataSet metadata")
p.add_argument("--anonymize", action="store_true",
help="Randomize sequences for privacy")
return p
def get_parser():
p = get_default_argparser_with_base_opts(
version="0.1",
description=__doc__)
p.add_argument("testkit_cfg")
p.add_argument("-u", "--host", dest="host", action="store",
default=os.environ.get("PB_SERVICE_HOST", "http://localhost"))
p.add_argument("-p", "--port", dest="port", action="store", type=int,
default=int(os.environ.get("PB_SERVICE_PORT", "8081")),
help="Services port number")
p.add_argument("-x", "--xunit", dest="xml_out", default="test-output.xml",
help="Output XUnit test results")
p.add_argument("-t", "--timeout", dest="time_out", type=int, default=1800,
help="Timeout for blocking after job submission")
p.add_argument("-s", "--sleep", dest="sleep", type=int, default=2,
help="Sleep time after job submission")
p.add_argument("--ignore-test-failures", dest="ignore_test_failures",
action="store_true",
help="Only exit with non-zero return code if the job "+
"itself failed, regardless of test outcome")
p.add_argument("--import-only", dest="import_only", action="store_true",
help="Import datasets without running pipeline")
p.add_argument("--only-tests", dest="test_job_id", action="store",
type=int, default=None,
help="Run tests on an existing smrtlink job")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(
version="0.1",
description=__doc__)
p.add_argument("testkit_cfg")
p.add_argument("-u", "--host", dest="host", action="store",
default="http://localhost")
p.add_argument("-p", "--port", dest="port", action="store", type=int,
default=8081, help="Port number")
p.add_argument("-x", "--xunit", dest="xml_out", default="test-output.xml",
help="Output XUnit test results")
p.add_argument("-t", "--timeout", dest="time_out", type=int, default=1800,
help="Timeout for blocking after job submission")
p.add_argument("-s", "--sleep", dest="sleep", type=int, default=2,
help="Sleep time after job submission")
p.add_argument("--ignore-test-failures", dest="ignore_test_failures",
action="store_true",
help="Only exit with non-zero return code if the job "+
"itself failed, regardless of test outcome")
p.add_argument("--import-only", dest="import_only", action="store_true",
help="Import datasets without running pipeline")
p.add_argument("--only-tests", dest="test_job_id", action="store",
type=int, default=None,
help="Run tests on an existing smrtlink job")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(
version="0.1",
description=__doc__)
p.add_argument("junit_file", nargs="+", type=argparse.FileType('r'))
p.add_argument("-o", "--output-file", dest="output_file", action="store",
default="junit_results_merged.xml")
return p
def get_parser():
"""Set up and return argument parser."""
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("in_fn", type=str, help="Input DataSet or DataStore")
p.add_argument("out_fn", type=str, help="Output DataSet or DataStore")
return p
def get_parser():
p = get_default_argparser_with_base_opts(version=VERSION,
description=__doc__,
default_level="WARN")
p.add_argument("input_bam",
help="Input BAM or DataSet from which reads will be read")
p.add_argument("output_bam",
nargs='?',
default=None,
help="Output BAM or DataSet to which filtered reads will "
"be written")
p.add_argument("--show-zmws",
action="store_true",
default=False,
help="Print a list of ZMWs and exit")
p.add_argument("--whitelist",
action="store",
default=None,
help="Comma-separated list of ZMWs, or file containing " +
"whitelist of one hole number per line, or " +
"BAM/DataSet file from which to extract ZMWs")
p.add_argument("--blacklist",
action="store",
default=None,
help="Opposite of --whitelist, specifies ZMWs to discard")
p.add_argument("--percentage",
action="store",
type=float,
default=None,
help="If you prefer to recover a percentage of a SMRTcell "
"rather than a specific list of reads specify that "
"percentage (range 0-100) here")
p.add_argument("-n",
"--count",
action="store",
type=int,
default=None,
help="Recover a specific number of ZMWs picked at random")
p.add_argument("-s",
"--seed",
action="store",
type=int,
default=None,
help="Random seed for selecting a percentage of reads")
p.add_argument("--ignore-metadata",
action="store_true",
help="Discard input DataSet metadata")
p.add_argument("--relative",
action="store_true",
help="Make external resource paths relative")
p.add_argument("--anonymize",
action="store_true",
help="Randomize sequences for privacy")
p.add_argument("--barcodes",
action="store_true",
help="Indicates that the whitelist or blacklist contains " +
"barcode indices instead of ZMW numbers")
return p
def get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__)
p.add_argument("testkit_cfg_fofn",
nargs="+",
type=argparse.FileType("r"),
help="Text file listing testkit.cfg files to run; you " +
"may provide more than one of these")
p.add_argument("-u",
"--host",
dest="host",
action="store",
default=Constants.HOST)
p.add_argument("-p",
"--port",
dest="port",
action="store",
default=Constants.PORT,
help="Port number")
p.add_argument("-n",
"--nworkers",
type=int,
default=Constants.NPROC,
help="Number of jobs to concurrently run.")
p.add_argument("-t",
"--timeout",
dest="time_out",
type=int,
default=1800,
help="Timeout for blocking after job submission")
p.add_argument("-s",
"--sleep",
dest="sleep",
type=int,
default=Constants.SLEEP_TIME,
help="Sleep time after job submission")
p.add_argument("--ignore-test-failures",
dest="ignore_test_failures",
action="store_true",
help="Only exit with non-zero return code if the job " +
"itself failed, regardless of test outcome")
p.add_argument("--import-only",
dest="import_only",
action="store_true",
help="Import datasets without running pipelines")
p.add_argument("-j",
"--junit-xml",
dest="junit_out",
action="store",
default="junit_combined_results.xml",
help="JUnit output file for all tests")
p.add_argument("-x",
"--nunit-xml",
dest="nunit_out",
action="store",
default="nunit_combined_results.xml",
help="NUnit output file for all tests")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("fastq_in", help="Input FASTQ file")
p.add_argument("summary_csv", help="Input Summary CSV file")
p.add_argument("subreads_in", help="Input SubreadSet XML")
p.add_argument("zip_out", help="Output ZIP file")
return p
def get_parser():
"""Define Parser. Use the helper methods in validators to validate input"""
p = get_default_argparser_with_base_opts(__version__, __doc__)
f = p.add_argument
f('path_to_file', type=validate_file, help="Path to File")
f('output_file', help="Path to output TXT file")
f('--nrecords', type=int, default=10, help="Number of records to write")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("consensus_in", help="Input consensus FASTQ file")
p.add_argument("chimeras_in", help="Input chimeras FASTQ file")
p.add_argument("subreads_in", help="Input SubreadSet XML")
p.add_argument("consensus_out", help="Output consensus ZIP file")
p.add_argument("chimeras_out", help="Output chimeras ZIP file")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(
version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("ccs_in", help="Input ConsensusReadSet")
p.add_argument("subreads_in", help="Input SubreadSet")
p.add_argument("ccs_out", help="Output ConsensusReadSet")
p.add_argument("--use-run-design-uuid", action="store_true", default=False,
help="Use pre-defined UUID generated by Run Design")
return p
def _get_parser():
desc = "Custom PipelineTemplate Registry to write pipeline templates to output directory"
p = get_default_argparser_with_base_opts(__version__,
desc,
default_level=logging.ERROR)
p.add_argument('output_dir', help="Path to output directory")
p.add_argument('--with-xml',
action="store_true",
default=False,
help="Also Write Pipeline Templates as XML")
return p
def get_parser():
desc = "Generate Pipeline documentation from a directory of Resolved Pipeline Templates"
p = get_default_argparser_with_base_opts(__version__, desc)
f = p.add_argument
f("pipeline_dir", type=validate_dir, help="Path to Pipeline Template JSON Dir")
f('-o', "--output-dir", default="pipeline-docs", help="Path to RST Output Dir")
f('-t', '--title', default="PacBio Pipelines", help="Title of Pipeline documents")
f('-d', '--doc-version', default="0.1.0", help="Version of Pipeline documents")
return p
def get_parser():
p = get_default_argparser_with_base_opts(__version__, "Stress Tool")
f = p.add_argument
f('--host', default="localhost", help="Host name")
f('--port', default=8070, type=int, help="Port")
f('-n', '--nprocesses', default=10, type=int, help="Number of worker processes to launch")
# FIXME this naming is terrible
f('-x', default=5, type=int, help="Total number of tasks will be ~ 3 x")
f('--profile', default="profile.json", help="Path to output profile.json")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("output_file", help="Gathered output file")
p.add_argument("chunked_files", nargs="+", help="Chunked input files")
p.add_argument("--join-contigs",
action="store_true",
default=False,
help="Merge split contigs")
p.add_argument("--dataset", help="Dataset XML for populating metadata")
return p
def get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("modifications", help="Base modification GFF file")
p.add_argument("alignmentSummary", help="Alignment summary GFF")
p.add_argument(
"gff_out",
help=
"Coverage summary for regions (bins) spanning the reference with basemod results for each region"
)
return p
def get_parser():
description = 'Run dataset.py by specifying a command.'
parser = get_default_argparser_with_base_opts(
version=__VERSION__,
description=description,
default_level="WARNING")
parser.add_argument("--strict", default=False, action='store_true',
help="Turn on strict tests, raise all errors")
parser.add_argument("--skipCounts", default=False, action='store_true',
help="Turn on strict tests, raise all errors")
subparser_list = get_subparsers()
parser = add_subparsers(parser, subparser_list)
return parser
def get_parser():
p = get_default_argparser_with_base_opts(__version__, __doc__)
f = p.add_argument
f('subreadset_path', type=validate_file, help="Path to SubreadSet XML")
f('--name', type=str, default="Auto Job Name", help="Job Name")
f('--host', type=str, default="smrtlink-beta", help="SMRT Link host")
f('--port', type=int, default=8081, help="SMRT Link port")
f('-r', '--reference-set-uuid', type=str, default=Constants.DEFAULT_RSET_UUID, help="ReferenceSet UUID")
f('-p', '--pipeline-id', type=str, default=Constants.DEFAULT_PIPELINE, help="Pipeline Id")
f('--block', default=False, action="store_true", help="Block and Wait for job to complete")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("merged", help="Name of merge datastore file")
p.add_argument("chunks", nargs="+", help="Chunk datastore outputs")
p.add_argument("-j",
"--nproc",
dest="nproc",
type=int,
default=1,
help="Number of processors to use")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(
version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument(
"input_reads", help="SubreadSet or ConsensusReadSet use as INPUT for lima")
p.add_argument("dataset_name", help="Dataset name")
p.add_argument("output_file", help="Output dataset XML")
p.add_argument("--biosamples-csv",
action="store",
default=None,
help="Optional CSV file containing Barcode/BioSample list")
return p
def get_parser():
desc = ""
parser = get_default_argparser_with_base_opts(
version=__version__, description=__doc__)
parser.add_argument('filter_summary_csv', type=validate_file,
help="Filter CSV file.")
parser.add_argument(
'-o', "--output", dest='output_dir', default=os.getcwd(), type=validate_dir,
help="Output directory for histogram images generated")
parser.add_argument('-r', '--report', dest='json_report',
help='Path of JSON report.')
parser.add_argument("--dpi", default=60, type=int,
help="dots/inch")
return parser
def get_parser():
desc = "Tool to import datasets, convert/import fasta file and run analysis jobs"
p = get_default_argparser_with_base_opts(__version__, desc)
sp = p.add_subparsers(help='commands')
def builder(subparser_id, description, options_func, exe_func):
subparser_builder(sp, subparser_id, description, options_func,
exe_func)
status_desc = "Get System Status, DataSet and Job Summary"
builder('status', status_desc, add_base_and_sal_options,
args_get_sal_summary)
local_desc = " The file location must be accessible from the host where the Services are running (often on a shared file system)"
ds_desc = "Import Local DataSet XML." + local_desc
builder('import-dataset', ds_desc, add_sal_and_xml_dir_options,
args_runner_import_datasets)
fasta_desc = "Import Fasta (and convert to ReferenceSet)." + local_desc
builder("import-fasta", fasta_desc, add_import_fasta_opts,
args_run_import_fasta)
run_analysis_desc = "Run Secondary Analysis Pipeline using an analysis.json"
builder("run-analysis", run_analysis_desc, add_run_analysis_job_opts,
args_run_analysis_job)
emit_analysis_json_desc = "Emit an analysis.json Template to stdout that can be run using 'run-analysis'"
builder("emit-analysis-template", emit_analysis_json_desc,
add_common_options, args_emit_analysis_template)
# Get Summary Job by Id
job_summary_desc = "Get Job Summary by Job Id"
builder('get-job', job_summary_desc, add_get_job_options,
args_get_job_summary)
job_list_summary_desc = "Get Job Summary by Job Id"
builder('get-jobs', job_list_summary_desc, add_get_job_list_options,
args_get_job_list_summary)
ds_summary_desc = "Get DataSet Summary by DataSet Id or UUID"
builder('get-dataset', ds_summary_desc, add_get_dataset_options,
args_run_dataset_summary)
ds_list_summary_desc = "Get DataSet List Summary by DataSet Type"
builder('get-datasets', ds_list_summary_desc, add_get_dataset_list_options,
args_run_dataset_list_summary)
return p
def get_parser():
"""Util func to create an argparse instance
Removing explicit usage due to issues with thirdparty argparse (Python < 2.7)
usage = "usage: %prog --input=inputRgn.Fofn --outputCsv=mySubreadSummary.csv"
"""
desc = 'Tool for generating a CSV file of the filtered Subreads from a file name of files (FOFN).'
parser = get_default_argparser_with_base_opts(
version=__version__, description=__doc__)
parser.add_argument('region_fofn', type=validate_fofn,
help='Input Region FOFN path')
parser.add_argument('-o', '--output-csv', default=None, dest='output_csv',
help='Output File to write summary to')
return parser
def get_parser():
description = 'Run dataset.py by specifying a command.'
parser = get_default_argparser_with_base_opts(version=__VERSION__,
description=description,
default_level="WARNING")
parser.add_argument("--strict",
default=False,
action='store_true',
help="Turn on strict tests, raise all errors")
parser.add_argument("--skipCounts",
default=False,
action='store_true',
help="Turn on strict tests, raise all errors")
subparser_list = get_subparsers()
parser = add_subparsers(parser, subparser_list)
return parser
def _get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument(
"dataset",
help="PacBio dataset XML (AlignmentSet or ConsensusAlignmentSet)")
p.add_argument("csv_out", help="CSV output file")
p.add_argument("--load-snr",
action="store_true",
default=False,
help="Include per-read SNRs")
p.add_argument("--load-numpasses",
action="store_true",
default=False,
help="Include numPasses (CCS only)")
return p
def get_parser():
description = 'Run dataset.py by specifying a command.'
parser = get_default_argparser_with_base_opts(version=__VERSION__,
description=description,
default_level="WARNING")
parser.add_argument("--strict",
default=False,
action='store_true',
help="Turn on strict tests, raise all errors")
parser.add_argument("--skipCounts",
default=False,
action='store_true',
help="Skip updating NumRecords and TotalLength counts")
subparser_list = get_subparsers()
parser = add_subparsers(parser, subparser_list)
msg = "Please specify a sub-command, or call with --help for more options"
parser.set_defaults(func=lambda args: parser.error(msg))
return parser
def get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__)
p.add_argument("testkit_cfg_fofn",
type=validate_testkit_cfg_fofn,
help="Text file listing testkit.cfg files to run")
p.add_argument("-u",
"--host",
dest="host",
action="store",
default=Constants.HOST)
p.add_argument("-p",
"--port",
dest="port",
action="store",
default=Constants.PORT,
help="Port number")
p.add_argument("-n",
"--nworkers",
type=int,
default=Constants.NPROC,
help="Number of jobs to concurrently run.")
p.add_argument("-t",
"--timeout",
dest="time_out",
type=int,
default=1800,
help="Timeout for blocking after job submission")
p.add_argument("-s",
"--sleep",
dest="sleep",
type=int,
default=2,
help="Sleep time after job submission")
p.add_argument("--ignore-test-failures",
dest="ignore_test_failures",
action="store_true",
help="Only exit with non-zero return code if the job " +
"itself failed, regardless of test outcome")
p.add_argument("--import-only",
dest="import_only",
action="store_true",
help="Import datasets without running pipelines")
return p
def get_parser():
"""Util func to create an argparse instance
Removing explicit usage due to issues with thirdparty argparse (Python < 2.7)
usage = "usage: %prog --input=inputRgn.Fofn --outputCsv=mySubreadSummary.csv"
"""
desc = 'Tool for generating a CSV file of the filtered Subreads from a file name of files (FOFN).'
parser = get_default_argparser_with_base_opts(version=__version__,
description=__doc__)
parser.add_argument('region_fofn',
type=validate_fofn,
help='Input Region FOFN path')
parser.add_argument('-o',
'--output-csv',
default=None,
dest='output_csv',
help='Output File to write summary to')
return parser
def _get_parser():
p = get_default_argparser_with_base_opts(
version="0.1",
description=__doc__)
p.add_argument("testkit_cfg")
p.add_argument("-u", "--host", dest="host", action="store",
default="http://localhost")
p.add_argument("-p", "--port", dest="port", action="store", type=int,
default=8081, help="Port number")
p.add_argument("-x", "--xunit", dest="xml_out", default="test-output.xml",
help="Output XUnit test results")
p.add_argument("-t", "--timeout", dest="time_out", type=int, default=1800,
help="Timeout for blocking after job submission")
p.add_argument("-s", "--sleep", dest="sleep", type=int, default=2,
help="Sleep time after job submission")
p.add_argument("--ignore-test-failures", dest="ignore_test_failures",
action="store_true",
help="Only exit with non-zero return code if the job "+
"itself failed, regardless of test outcome")
return p
def get_parser():
p = get_default_argparser_with_base_opts(
version=VERSION,
description=__doc__,
default_level="WARN")
p.add_argument("input_bam",
help="Input BAM or DataSet from which reads will be read")
p.add_argument("output_bam", nargs='?', default=None,
help="Output BAM or DataSet to which filtered reads will "
"be written")
p.add_argument("--show-zmws", action="store_true", default=False,
help="Print a list of ZMWs and exit")
p.add_argument("--whitelist", action="store", default=None,
help="Comma-separated list of ZMWs, or file containing " +
"whitelist of one hole number per line, or " +
"BAM/DataSet file from which to extract ZMWs")
p.add_argument("--blacklist", action="store", default=None,
help="Opposite of --whitelist, specifies ZMWs to discard")
p.add_argument("--percentage", action="store", type=float, default=None,
help="If you prefer to recover a percentage of a SMRTcell "
"rather than a specific list of reads specify that "
"percentage (range 0-100) here")
p.add_argument("-n", "--count", action="store", type=int, default=None,
help="Recover a specific number of ZMWs picked at random")
p.add_argument("-s", "--seed", action="store", type=int, default=None,
help="Random seed for selecting a percentage of reads")
p.add_argument("--ignore-metadata", action="store_true",
help="Discard input DataSet metadata")
p.add_argument("--relative", action="store_true",
help="Make external resource paths relative")
p.add_argument("--anonymize", action="store_true",
help="Randomize sequences for privacy")
p.add_argument("--barcodes", action="store_true",
help="Indicates that the whitelist or blacklist contains "+
"barcode indices instead of ZMW numbers")
p.add_argument("--sample-scraps", action="store_true",
help="If enabled, --percentage and --count will include "+
"hole numbers from scraps BAM files when picking a "+
"random sample (default is to sample only ZMWs "+
"present in subreads BAM).")
return p
def get_parser():
p = get_default_argparser_with_base_opts(
version=__version__,
description=__doc__)
p.add_argument("testkit_cfg_fofn", type=validate_testkit_cfg_fofn,
help="Text file listing testkit.cfg files to run")
p.add_argument("-u", "--host", dest="host", action="store",
default=Constants.HOST)
p.add_argument("-p", "--port", dest="port", action="store",
default=Constants.PORT, help="Port number")
p.add_argument("-n", "--nworkers", type=int, default=Constants.NPROC,
help="Number of jobs to concurrently run.")
p.add_argument("-t", "--timeout", dest="time_out", type=int, default=1800,
help="Timeout for blocking after job submission")
p.add_argument("-s", "--sleep", dest="sleep", type=int, default=2,
help="Sleep time after job submission")
p.add_argument("--ignore-test-failures", dest="ignore_test_failures",
action="store_true",
help="Only exit with non-zero return code if the job "+
"itself failed, regardless of test outcome")
return p
def get_parser():
"""Old Usage in pbpy:
usage = filter_subread.py --debug filtered_subread_summary.csv --output /path/to/outputDir --report /path/to/outputDir/junk3.json
filtered_subread_summary.csv
"""
desc = ""
parser = get_default_argparser_with_base_opts(
version=__version__, description=__doc__)
parser.add_argument("filter_summary_csv",
help="Path to Filter Subread Summary CSV file.",
type=validate_file)
parser.add_argument('-o', '--output', dest='output', default=os.getcwd(),
type=validate_dir,
help='Output directory to write to Subread Hist plots to.')
parser.add_argument('--dpi', type=int, dest='dpi', default=72,
help="dpi (dots/inch) for plots that were generated.")
parser.add_argument('-r', '--report', dest='report', default=None,
help="Write the Json report to disk.")
return parser
def _get_parser():
p = get_default_argparser_with_base_opts(
version=__VERSION__,
description=__doc__,
default_level="INFO")
p.add_argument("mode", choices=["consolidate", "fasta", "fastq"])
p.add_argument("dataset_file")
p.add_argument("datastore_out")
p.add_argument("--min-rq",
dest="min_rq",
type=float,
default=Constants.HIFI_RQ,
help="Sets RQ cutoff for splitting output")
p.add_argument("--min-qv",
dest="min_rq",
type=lambda arg: phred_qv_as_accuracy(int(arg)),
help="Alternative to --min-rq, on Phred scale (0-60)")
p.add_argument("--no-zip",
action="store_true",
help="Disable ZIP output")
return p
def get_parser():
desc = "Generate Pipeline documentation from a directory of Resolved Pipeline Templates"
p = get_default_argparser_with_base_opts(__version__, desc)
f = p.add_argument
f("pipeline_dir",
type=validate_dir,
help="Path to Pipeline Template JSON Dir")
f('-o',
"--output-dir",
default="pipeline-docs",
help="Path to RST Output Dir")
f('-t',
'--title',
default="PacBio Pipelines",
help="Title of Pipeline documents")
f('-d',
'--doc-version',
default="0.1.0",
help="Version of Pipeline documents")
return p
def get_parser():
desc = "Tool to import datasets, convert/import fasta file and run analysis jobs"
p = get_default_argparser_with_base_opts(__version__, desc)
sp = p.add_subparsers(help='commands')
def builder(subparser_id, description, options_func, exe_func):
subparser_builder(sp, subparser_id, description, options_func, exe_func)
status_desc = "Get System Status, DataSet and Job Summary"
builder('status', status_desc, add_base_and_sal_options, args_get_sal_summary)
local_desc = " The file location must be accessible from the host where the Services are running (often on a shared file system)"
ds_desc = "Import Local DataSet XML." + local_desc
builder('import-dataset', ds_desc, add_sal_and_xml_dir_options, args_runner_import_datasets)
fasta_desc = "Import Fasta (and convert to ReferenceSet)." + local_desc
builder("import-fasta", fasta_desc, add_import_fasta_opts, args_run_import_fasta)
run_analysis_desc = "Run Secondary Analysis Pipeline using an analysis.json"
builder("run-analysis", run_analysis_desc, add_run_analysis_job_opts, args_run_analysis_job)
emit_analysis_json_desc = "Emit an analysis.json Template to stdout that can be run using 'run-analysis'"
builder("emit-analysis-template", emit_analysis_json_desc, add_common_options, args_emit_analysis_template)
# Get Summary Job by Id
job_summary_desc = "Get Job Summary by Job Id"
builder('get-job', job_summary_desc, add_get_job_options, args_get_job_summary)
job_list_summary_desc = "Get Job Summary by Job Id"
builder('get-jobs', job_list_summary_desc, add_get_job_list_options, args_get_job_list_summary)
ds_summary_desc = "Get DataSet Summary by DataSet Id or UUID"
builder('get-dataset', ds_summary_desc, add_get_dataset_options, args_run_dataset_summary)
ds_list_summary_desc = "Get DataSet List Summary by DataSet Type"
builder('get-datasets', ds_list_summary_desc, add_get_dataset_list_options, args_run_dataset_list_summary)
return p
def get_parser():
sample_picker = {'first': sample_first,
'random': sample_random,
'uniform': sample_uniform}
p = get_default_argparser_with_base_opts(
version=__version__,
description=__doc__,
default_level="WARN")
p.add_argument('subreadset', type=SubreadSet,
help="Input SubreadSet for an Internal BAM")
p.add_argument('alignmentset', type=AlignmentSet,
help="Input AlignmentSet for the SubreadSet")
p.add_argument('outprefix', type=str,
help="Output prefix for csvs")
p.add_argument('--nreads', type=int,
help="The number of reads to process")
p.add_argument('--sampler', default='uniform',
type=lambda x: sample_picker.get(x),
choices=sample_picker.keys(),
help="Read sampling mechanism")
p.add_argument('--search', type=int, default=25,
help=('Limit the number of hns to search for a '
'local hit'))
return p
def _get_parser():
p = get_default_argparser_with_base_opts(
version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument(
"input_reads", help="SubreadSet or ConsensusReadSet use as INPUT for lima")
p.add_argument(
"lima_datastore", help="Datastore json generated by lima to demultiplex input_reads.")
p.add_argument(
"barcodes", help="BarcodeSet lima used to demultiplex reads")
p.add_argument("out_json", help="Output datastore json")
p.add_argument("--isoseq-mode", action="store_true", default=False,
help="Iso-Seq mode")
p.add_argument("--use-barcode-uuids", action="store_true", default=False,
help="Apply pre-defined barcoded dataset UUIDs from input_reads")
p.add_argument("--min-bq-filter", action="store", type=int,
default=Constants.BARCODE_QUALITY_GREATER_THAN,
help="Minimum barcode quality encoded in dataset filter")
p.add_argument("-j", "--nproc", dest="nproc", action="store", type=int,
default=1, help="Number of processors to use")
p.add_argument("--outdir", action="store", default=None,
help="Output directory for update datasets")
return p
def _get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__)
p.add_argument("subreads", type=validate_file)
p.add_argument("datastore", type=_validate_output_file)
return p
def get_parser():
"""Define Parser. Use the helper methods in validators to validate input"""
p = get_default_argparser_with_base_opts(__version__, __doc__)
p.add_argument('path_to_file', type=validate_file, help="Path to File")
return p
def get_base_parser(description, log_level="INFO"):
from pbcommand.cli import get_default_argparser_with_base_opts
from pbcoretools import __VERSION__
return get_default_argparser_with_base_opts(version=__VERSION__,
description=description,
default_level=log_level)
def get_parser():
p = get_default_argparser_with_base_opts(version="0.1",
description=__doc__)
p.add_argument("testkit_cfg")
p.add_argument(
"-u",
"--host",
dest="host",
action="store",
default=os.environ.get("PB_SERVICE_HOST", "localhost"),
help=
"Hostname of SMRT Link server. If this is anything other than 'localhost' you must supply authentication."
)
p.add_argument("-p",
"--port",
dest="port",
action="store",
type=int,
default=int(os.environ.get("PB_SERVICE_PORT", "8081")),
help="Services port number")
p.add_argument("--user",
dest="user",
action="store",
default=os.environ.get("PB_SERVICE_AUTH_USER", None),
help="User to authenticate with (if using HTTPS)")
p.add_argument("--password",
dest="password",
action="store",
default=os.environ.get("PB_SERVICE_AUTH_PASSWORD", None),
help="Password to authenticate with (if using HTTPS)")
p.add_argument("-x",
"--xunit",
dest="xml_out",
default="test-output.xml",
help="Output XUnit test results")
p.add_argument(
"-n",
"--nunit",
dest="nunit_out",
default="nunit_out.xml",
help=
"Optional NUnit output file, used for JIRA/Xray integration; will be written only if the 'xray_tests' field is populated."
)
p.add_argument("-t",
"--timeout",
dest="time_out",
type=int,
default=1800,
help="Timeout for blocking after job submission")
p.add_argument("-s",
"--sleep",
dest="sleep",
type=int,
default=2,
help="Sleep time after job submission")
p.add_argument("--ignore-test-failures",
dest="ignore_test_failures",
action="store_true",
help="Only exit with non-zero return code if the job " +
"itself failed, regardless of test outcome")
p.add_argument("--import-only",
dest="import_only",
action="store_true",
help="Import datasets without running pipeline")
p.add_argument("--only-tests",
dest="test_job_id",
action="store",
type=int,
default=None,
help="Run tests on an existing smrtlink job")
return p
def get_parser():
"""Define Parser. Use the helper methods in validators to validate input"""
p = get_default_argparser_with_base_opts(__version__, __doc__)
p.add_argument('path_to_file', type=validate_file, help="Path to File")
return p
def get_parser():
p = get_default_argparser_with_base_opts(version=VERSION,
description=__doc__,
default_level="WARN")
p.add_argument("input_bam",
help="Input BAM or DataSet from which reads will be read")
p.add_argument("output_bam",
nargs='?',
default=None,
help="Output BAM or DataSet to which filtered reads will "
"be written")
p.add_argument("--show-zmws",
action="store_true",
default=False,
help="Print a list of ZMWs and exit")
p.add_argument("--whitelist",
action="store",
default=None,
help="Comma-separated list of ZMWs, or file containing " +
"whitelist of one hole number per line, or " +
"BAM/DataSet file from which to extract ZMWs")
p.add_argument("--blacklist",
action="store",
default=None,
help="Opposite of --whitelist, specifies ZMWs to discard")
p.add_argument(
"--subreads",
action="store_true",
help="If set, the whitelist or blacklist will be assumed to contain " +
"one subread name per line, or " +
"a BAM/DataSet file from which to extract subreads")
p.add_argument("--percentage",
action="store",
type=float,
default=None,
help="If you prefer to recover a percentage of a SMRTcell "
"rather than a specific list of reads specify that "
"percentage (range 0-100) here")
p.add_argument("-n",
"--count",
action="store",
type=int,
default=None,
help="Recover a specific number of ZMWs picked at random")
p.add_argument("-s",
"--seed",
action="store",
type=int,
default=None,
help="Random seed for selecting a percentage of reads")
p.add_argument("--ignore-metadata",
action="store_true",
help="Discard input DataSet metadata")
p.add_argument("--relative",
action="store_true",
help="Make external resource paths relative")
p.add_argument("--anonymize",
action="store_true",
help="Randomize sequences for privacy")
p.add_argument("--barcodes",
action="store_true",
help="Indicates that the whitelist or blacklist contains " +
"barcode indices instead of ZMW numbers")
p.add_argument("--sample-scraps",
action="store_true",
help="If enabled, --percentage and --count will include " +
"hole numbers from scraps BAM files when picking a " +
"random sample (default is to sample only ZMWs " +
"present in subreads BAM).")
p.add_argument("--keep-uuid",
action="store_true",
help="If enabled, the UUID from the input dataset will " +
"be used for the output as well.")
p.add_argument("--min-adapters",
action="store",
type=int,
default=None,
help="Minimum number of adapters to filter for")
return p
def _get_parser():
desc = "Custom PipelineTemplate Registry to write pipeline templates to output directory"
p = get_default_argparser_with_base_opts(__version__, desc, default_level=logging.ERROR)
p.add_argument('output_dir', help="Path to output directory")
p.add_argument('--with-xml', action="store_true", default=False, help="Also Write Pipeline Templates as XML")
return p
def get_parser():
p = get_default_argparser_with_base_opts(version=__version__,
description=__doc__,
default_level="INFO")
p.add_argument("alignment_set", help="BAM or Alignment DataSet")
p.add_argument("--reference",
action="store",
required=True,
type=validateFile,
help="Fasta or Reference DataSet")
p.add_argument("--gff",
action="store",
default=None,
help="Output GFF file of modified bases")
p.add_argument("--csv",
action="store",
default=None,
help="Output CSV file out per-nucleotide information")
p.add_argument(
"--bigwig",
action="store",
default=None,
help="Output BigWig file encoding IpdRatio for both strands")
# FIXME use central --nproc option
p.add_argument('--numWorkers',
'-j',
dest='numWorkers',
default=1,
type=int,
help='Number of thread to use (-1 uses all logical cpus)')
# common options
p.add_argument("--pvalue",
type=float,
default=Constants.PVALUE_DEFAULT,
help="P-value cutoff")
p.add_argument("--maxLength",
type=int,
default=Constants.MAX_LENGTH_DEFAULT,
help="Maximum number of bases to process per contig")
p.add_argument(
"--identify",
action="store",
default="m6A,m4C",
help="Specific modifications to identify (comma-separated " +
"list). Currrent options are m6A, m4C, m5C_TET. Using --control " +
"overrides this option.")
_DESC = "In the --identify mode, add --methylFraction to " +\
"command line to estimate the methylated fraction, along with " +\
"95%% confidence interval bounds."
p.add_argument("--methylFraction", action="store_true", help=_DESC)
p.add_argument(
'--outfile',
dest='outfile',
default=None,
help=
'Use this option to generate all possible output files. Argument here is the root filename of the output files.'
)
# FIXME: Need to add an extra check for this; it can only be used if
# --useLDA flag is set.
p.add_argument('--m5Cgff',
dest='m5Cgff',
default=None,
help='Name of output GFF file containing m5C scores')
# FIXME: Make sure that this is specified if --useLDA flag is set.
p.add_argument('--m5Cclassifier',
dest='m5Cclassifier',
default=None,
help='Specify csv file containing a 127 x 2 matrix')
p.add_argument('--pickle',
dest='pickle',
default=None,
help='Name of output pickle file.')
p.add_argument('--ms_csv',
dest='ms_csv',
default=None,
help='Multisite detection CSV file.')
# Calculation options:
p.add_argument(
'--control',
dest='control',
default=None,
type=validateNoneOrFile,
help=
'AlignmentSet or mapped BAM file containing a control sample. Tool will perform a case-control analysis'
)
# Temporary addition to test LDA for Ca5C detection:
p.add_argument('--useLDA',
action="store_true",
dest='useLDA',
default=False,
help='Set this flag to debug LDA for m5C/Ca5C detection')
# Parameter options:
defaultParamsPathSpec = _getResourcePathSpec()
p.add_argument(
'--paramsPath',
dest='paramsPath',
default=defaultParamsPathSpec,
type=validateNoneOrPathSpec,
help=
'List of :-delimited directory paths containing in-silico trained models (default is "%s")'
% defaultParamsPathSpec)
# XXX hacky workaround for running tests using obsolete chemistry inputs
p.add_argument("--useChemistry",
dest="useChemistry",
default=None,
help=argparse.SUPPRESS)
p.add_argument('--minCoverage',
dest='minCoverage',
default=3,
type=int,
help='Minimum coverage required to call a modified base')
p.add_argument('--maxQueueSize',
dest='maxQueueSize',
default=20,
type=int,
help='Max Queue Size')
p.add_argument('--maxCoverage',
dest='maxCoverage',
type=int,
default=-1,
help='Maximum coverage to use at each site')
p.add_argument('--mapQvThreshold',
dest='mapQvThreshold',
type=float,
default=-1.0)
p.add_argument('--ipdModel',
dest='ipdModel',
default=None,
type=validateNoneOrFile,
help='Alternate synthetic IPD model HDF5 file')
p.add_argument('--modelIters',
dest='modelIters',
type=int,
default=-1,
help='[Internal] Number of GBM model iteration to use')
p.add_argument('--cap_percentile',
dest='cap_percentile',
type=float,
default=99.0,
help='Global IPD percentile to cap IPDs at')
p.add_argument(
"--methylMinCov",
type=int,
dest='methylMinCov',
default=10,
help=
"Do not try to estimate methylFraction unless coverage is at least this."
)
p.add_argument(
"--identifyMinCov",
type=int,
dest='identifyMinCov',
default=5,
help=
"Do not try to identify the modification type unless coverage is at least this."
)
p.add_argument(
"--maxAlignments",
type=int,
dest="maxAlignments",
default=1500,
help="Maximum number of alignments to use for a given window")
# Computation management options:
p.add_argument("-w", "--referenceWindow", "--referenceWindows",
"--refContigs", # backwards compatibility
type=str,
dest='referenceWindowsAsString',
default=None,
help="The window (or multiple comma-delimited windows) of the reference to " + \
"be processed, in the format refGroup[:refStart-refEnd] " + \
"(default: entire reference).")
def slurpWindowFile(fname):
return ",".join(map(str.strip, open(fname).readlines()))
p.add_argument(
"--refContigIndex",
type=int,
dest='refContigIndex',
default=-1,
help=
"For debugging purposes only - rather than enter a reference contig name, simply enter an index"
)
p.add_argument(
"-W",
"--referenceWindowsFile",
"--refContigsFile", # backwards compatibility
type=slurpWindowFile,
dest='referenceWindowsAsString',
default=None,
help="A file containing reference window designations, one per line")
p.add_argument(
"--skipUnrecognizedContigs",
type=bool,
default=False,
help=
"Whether to skip, or abort, unrecognized contigs in the -w/-W flags")
# FIXME shouldn't it always do this?
p.add_argument("--alignmentSetRefWindows",
action="store_true",
dest="referenceWindowsFromAlignment",
help="Use refWindows in dataset")
# Debugging help options:
p.add_argument("--profile",
action="store_true",
dest="doProfiling",
default=False,
help="Enable Python-level profiling (using cProfile).")
add_debug_option(p)
p.add_argument(
"--seed",
action="store",
dest="randomSeed",
type=int,
default=None,
help="Random seed (for development and debugging purposes only)")
p.add_argument("--referenceStride",
action="store",
type=int,
default=1000,
help="Size of reference window in internal " +
"parallelization. For testing purposes only.")
return p
