def createXml(args):
if args.dsType is None:
dset = openDataFile(*args.infile,
strict=args.strict,
skipCounts=args.skipCounts,
generateIndices=args.generateIndices)
else:
dsTypes = DataSet.castableTypes()
dset = dsTypes[args.dsType](*args.infile,
strict=args.strict,
skipCounts=args.skipCounts,
generateIndices=args.generateIndices)
if args.generateIndices:
# we generated the indices with the last open, lets capture them with
# this one:
dset = dsTypes[args.dsType](*args.infile,
strict=args.strict,
skipCounts=args.skipCounts)
if args.dsName != '':
dset.name = args.dsName
log.debug("Dataset created")
dset.write(args.outfile,
validate=args.novalidate,
modPaths=True,
relPaths=args.relative)
log.debug("Dataset written")
return 0
def createXml(args):
dsTypes = DataSet.castableTypes()
dset = dsTypes[args.dsType](*args.infile, strict=args.strict,
skipCounts=args.skipCounts)
log.debug("Dataset created")
dset.write(args.outfile, validate=args.novalidate, modPaths=True,
relPaths=args.relative)
log.debug("Dataset written")
def createXml(args):
dsTypes = DataSet.castableTypes()
dset = dsTypes[args.dsType](
*args.infile, strict=args.strict, skipCounts=args.skipCounts, generateIndices=args.generateIndices
)
if args.generateIndices:
# we generated the indices with the last open, lets capture them with
# this one:
dset = dsTypes[args.dsType](*args.infile, strict=args.strict, skipCounts=args.skipCounts)
log.debug("Dataset created")
dset.write(args.outfile, validate=args.novalidate, modPaths=True, relPaths=args.relative)
log.debug("Dataset written")
def createXml(args):
if os.path.exists(args.outfile) and not args.force:
raise IOError("Output file {} already exists. Use --force to "
"clobber".format(args.outfile))
if args.dsType is None:
dset = openDataFile(*args.infile,
strict=args.strict,
skipCounts=args.skipCounts,
trustCounts=args.trustCounts,
generateIndices=args.generateIndices,
referenceFastaFname=args.reference_fasta_fname)
else:
dsTypes = DataSet.castableTypes()
dset = dsTypes[args.dsType](
*args.infile,
strict=args.strict,
skipCounts=args.skipCounts,
trustCounts=args.trustCounts,
generateIndices=args.generateIndices,
referenceFastaFname=args.reference_fasta_fname)
if args.dsName != '':
dset.name = args.dsName
if args.metadata:
dset.loadMetadata(args.metadata)
if args.well_sample_name or args.bio_sample_name:
if args.metadata:
log.warning(
"Setting the WellSample or BioSample name will overwrite fields pulled from %s",
args.metadata)
n_new_collections = add_mock_collection_metadata(dset)
if n_new_collections > 0:
log.warning(
"Created new CollectionMetadata from blank template for %d movies",
n_new_collections)
if args.well_sample_name:
force_set_all_well_sample_names(dset, args.well_sample_name)
if args.bio_sample_name:
force_set_all_bio_sample_names(dset, args.bio_sample_name)
log.debug("Dataset created")
if isinstance(dset, ContigSet):
if args.organism:
dset.metadata.organism = args.organism
if args.ploidy:
dset.metadata.ploidy = args.ploidy
dset.newUuid()
if args.no_sub_datasets:
dset.subdatasets = []
if args.unique_collections:
uniqueify_collections(dset.metadata)
dset.write(args.outfile, validate=args.novalidate, relPaths=args.relative)
log.debug("Dataset written")
return 0
def createXml(args):
if args.dsType is None:
dset = openDataFile(*args.infile, strict=args.strict,
skipCounts=args.skipCounts,
generateIndices=args.generateIndices)
else:
dsTypes = DataSet.castableTypes()
dset = dsTypes[args.dsType](*args.infile, strict=args.strict,
skipCounts=args.skipCounts,
generateIndices=args.generateIndices)
if args.generateIndices:
# we generated the indices with the last open, lets capture them with
# this one:
dset = dsTypes[args.dsType](*args.infile, strict=args.strict,
skipCounts=args.skipCounts)
if args.dsName != '':
dset.name = args.dsName
if args.metadata:
dset.loadMetadata(args.metadata)
log.debug("Dataset created")
dset.write(args.outfile, validate=args.novalidate, relPaths=args.relative)
log.debug("Dataset written")
return 0
def createXml(args):
dsTypes = DataSet.castableTypes()
dset = dsTypes[args.dsType](*args.infile)
log.debug("Dataset created")
dset.write(args.outfile, validate=args.novalidate, relPaths=args.relative)
log.debug("Dataset written")
def createXml(args):
dsTypes = DataSet.castableTypes()
dset = dsTypes[args.dsType](*args.infile)
log.debug("Dataset created")
dset.write(args.outfile, validate=args.novalidate, relPaths=args.relative)
log.debug("Dataset written")
def create_options(parser):
parser.description = ('Create an XML file from fofn, BAM, or DataSet XML '
'files.')
pad = parser.add_argument
pad("outfile", help="The XML file to create")
pad("infile",
nargs='+',
help=("The fofn, BAM, or XML file(s) to make into a DataSet XML"))
pad("--force",
default=False,
action='store_true',
help=("Clobber output file if it already exists"))
pad("--type",
type=str,
dest='dsType',
choices=DataSet.castableTypes(),
help=("The type of XML to create (may be inferred "
"if not provided). "))
pad("--name",
default='',
dest='dsName',
help="The name (in metadata) of the new DataSet")
pad("--generateIndices",
action='store_true',
default=False,
help=("Generate index files (.pbi and .bai for BAM, .fai for FASTA). "
"Requires pysam and pbindex."))
pad("--metadata",
help=("A Sequel metadata.xml file (or DataSet) to supply metadata"))
pad("--novalidate",
action='store_false',
default=True,
help=("Don't validate the resulting XML, don't modify paths"))
pad("--relative",
action='store_true',
default=False,
help=("Make the included paths relative instead of "
"absolute (not compatible with --novalidate)"))
pad("--organism",
action="store",
default="unknown",
help="Organism name (for ReferenceSet only)")
pad("--ploidy",
action="store",
default="haploid",
help="Genome ploidy (for ReferenceSet only)")
pad("--well-sample-name",
help=("Set the WellSample name for all movies (will generate new "
"CollectionMetadata from blank template for any movies that are "
"not already represented)."))
pad("--bio-sample-name",
help=("Set the BioSample name for all movies (will generate new "
"CollectionMetadata from blank template for any movies that are "
"not already represented)."))
pad("--reference-fasta-fname",
help=("A path to a reference fasta file for the new AlignmentSet"))
pad("--no-sub-datasets",
action="store_true",
default=False,
help="Don't nest sub-datasets in output XML")
pad("--unique-collections",
action="store_true",
default=False,
help="Make sure CollectionMetadata records are unique")
pad("--trustCounts",
action="store_true",
default=False,
help="Assuming record counts in input dataset are correct, and " +
"skip reading index files to get overall count")
parser.set_defaults(func=createXml)
