def make_parser():
parser = argparse.ArgumentParser(
description="Generates a condor dagman script from a provided "
"library metadata file."
)
parser.add_argument('-o', '--output', default='run.dagman',
help='Name to save master dagman too')
add_metadata_arguments(parser)
parser.add_argument(
'other_libraries', nargs='*',
help="(Deprecated) specify a list of library metadata file names."
)
parser.add_argument(
'-s', '--sep', choices=['TAB', ','], default='TAB',
help="Specify the field separator character in the library metadata file"
)
add_default_path_arguments(parser)
add_version_argument(parser)
add_debug_arguments(parser)
parser.add_argument('--splice-template',
help='override splice dagman template')
parser.add_argument('--collection-template', default='full-encode.dagman',
help='override collection dagman template')
return parser
def make_parser():
parser = argparse.ArgumentParser()
parser.add_argument('-w',
'--web-root',
required=True,
help='base url for tracks')
parser.add_argument('--root',
default=os.getcwd(),
help='root directory to search for tracks')
parser.add_argument('--bigwig',
action='store_true',
default=False,
help='generate track blocks for bigwigs')
parser.add_argument('--bam',
action='store_true',
default=False,
help='generate track blocks for bam files')
parser.add_argument('-s', '--sep', choices=['TAB', ','], default='TAB')
parser.add_argument('-l', '--libraries', action='append', default=[])
add_version_argument(parser)
add_debug_arguments(parser)
return parser
def main(cmdline=None):
parser = ArgumentParser()
parser.add_argument('-n',
'--experiment-name',
required=True,
help='Experiment name to select')
add_metadata_arguments(parser)
add_debug_arguments(parser)
args = parser.parse_args(cmdline)
configure_logging(args)
header_printed = False
libraries = load_library_tables(args.libraries)
experiments = load_experiments(args.experiments)
replicates = experiments.loc[args.experiment_name, 'replicates']
for i, (library_id,
library) in enumerate(libraries.loc[replicates].iterrows()):
filename = find_library_bam_file(library)
LOGGER.info(' Reading %s %d/%d', filename, i + 1, len(replicates))
mode = get_mode(filename, 'r')
with pysam.AlignmentFile(filename, mode) as alignment:
if not header_printed:
print(str(alignment.header))
header_printed = True
for read in alignment:
print(read.to_string())
def make_parser():
parser = argparse.ArgumentParser()
parser.add_argument('-s', '--sep', choices=['TAB',','], default='TAB')
parser.add_argument('libraries', nargs='*')
add_default_path_arguments(parser)
add_version_argument(parser)
add_debug_arguments(parser)
return parser
def make_parser():
parser = ArgumentParser()
parser.add_argument('--bam', required=True, help='Source bam file')
parser.add_argument('--prefix', help='set output name prefix')
parser.add_argument('--stranded',
action='store_true',
default=False,
help='Process as stranded data')
parser.add_argument('--reference-prefix', default='chr')
add_default_path_arguments(parser)
add_debug_arguments(parser)
return parser
def make_parser():
parser = argparse.ArgumentParser(
description="Write combined CSV for gene counts produced by STAR.")
parser.add_argument('-c', '--strand',
choices=['U', '+', '-'],
default='U',
help='which strand to use.')
parser.add_argument('-l', '--libraries', action='append', required=True,
help='library information table')
parser.add_argument('-e', '--experiments', action='append', required=True,
help='experiment information table')
parser.add_argument('-s', '--sep', choices=['TAB', ','], default='TAB')
parser.add_argument('--output-format', choices=['TAB', ','], default=',')
parser.add_argument('--gtf-cache', help='Specify name of GTF cache file')
parser.add_argument('--add-names', action='store_true', default=False,
help='Add names to ouptut quantification file')
add_debug_arguments(parser)
return parser
def make_parser():
parser = argparse.ArgumentParser(
description="Write combined CSV for a specific quantification.")
parser.add_argument('-q', '--quantification',
choices=['FPKM', 'TPM', 'expected_count',
'effective_length', 'length'],
default='FPKM',
help='which quantification value to use')
parser.add_argument('-l', '--libraries', action='append', required=True,
help='library information table')
parser.add_argument('-e', '--experiments', action='append', required=True,
help='experiment information table')
parser.add_argument('-s', '--sep', choices=['TAB', ','], default='TAB')
parser.add_argument('--output-format', choices=['TAB', ','], default=',')
parser.add_argument('--transcriptome', action='store_true', default=False,
help='Use RSEM transcriptome quantifications instead of genomic quantifications')
parser.add_argument('--gtf-cache', help='Specify name of GTF cache file')
parser.add_argument('--add-names', action='store_true', default=False,
help='Add names to ouptut quantification file')
add_debug_arguments(parser)
return parser
def make_parser():
parser = argparse.ArgumentParser(description="Write combined CSV for a specific quantification.")
parser.add_argument(
"-q",
"--quantification",
choices=["FPKM", "TPM", "expected_count", "effective_length", "length"],
default="FPKM",
help="which quantification value to use",
)
parser.add_argument("-l", "--libraries", action="append", help="library information table")
parser.add_argument("-e", "--experiments", action="append", help="experiment information table")
parser.add_argument("-s", "--sep", choices=["TAB", ","], default="TAB")
parser.add_argument("--output-format", choices=["TAB", ","], default=",")
parser.add_argument(
"--transcriptome",
action="store_true",
default=False,
help="Use RSEM transcriptome quantifications instead of genomic quantifications",
)
add_debug_arguments(parser)
return parser
def make_parser():
parser = argparse.ArgumentParser(
description=
"Write combined CSV for a specific quantification produced by RSEM.")
parser.add_argument('-q',
'--quantification',
choices=[
'FPKM', 'TPM', 'expected_count',
'effective_length', 'length'
],
default=[],
action='append',
help='which quantification value to use')
parser.add_argument('-l',
'--libraries',
action='append',
required=True,
help='library metadata table')
parser.add_argument('-e',
'--experiments',
action='append',
required=True,
help='experiment metadata table')
parser.add_argument('-s', '--sep', choices=['TAB', ','], default='TAB')
parser.add_argument('--output-format', choices=['TAB', ','], default=',')
parser.add_argument(
'--transcriptome',
action='store_true',
default=False,
help=
'Use RSEM transcriptome quantifications instead of genomic quantifications'
)
parser.add_argument('--genome-dir', help='Specify genome directory root')
parser.add_argument(
'--add-names',
action='store_true',
default=False,
help='Add names to ouptut quantification file, requires --gtf-cache')
add_debug_arguments(parser)
return parser
def make_parser():
parser = argparse.ArgumentParser()
parser.add_argument('--genome-dir',
required=True,
help='root for genome indexes')
parser.add_argument('-e',
'--experiments',
action='append',
default=[],
help='experiments table')
parser.add_argument('-l',
'--libraries',
action='append',
default=[],
help='library information tables')
parser.add_argument('-n',
'--use-experiment',
help='plot specific experiment name')
parser.add_argument('-q',
'--quantification',
default='TPM',
help='Specify quantification type to use')
parser.add_argument('-o',
'--output',
default='genesdetected.html',
help='output filename')
parser.add_argument('--gene-type-filter',
default=[],
action='append',
help='GENCODE gene_types to include')
parser.add_argument('--gene-list-filter',
default=None,
help='Filename to load a list of IDs to filter on')
parser.add_argument(
'filenames',
nargs='*',
help='Combined quantification file: libraries by genes')
add_debug_arguments(parser)
return parser