def start_cli():
parser = OptionParser(description='RefSeqCheck v{}'.format(__version__),
usage='CARTtools/refseqcheck <options>',
version=__version__)
parser.add_option('--input',
default=None,
dest='input',
action='store',
help='Input RefSeq database file (output of RefSeqDB)')
parser.add_option('--reference',
default=None,
dest='reference',
action='store',
help='Reference genome fasta file')
parser.add_option('--output',
default='output.txt',
dest='output',
action='store',
help='Output file name')
(options, args) = parser.parse_args()
welcome('RefSeqCheck')
toplevel.run(options)
goodbye('RefSeqCheck')
def start_cli():
parser = OptionParser(description='RefSeqDB v{}'.format(__version__),
usage='CARTtools/refseqdb <options>',
version=__version__)
parser.add_option('--build',
default='GRCh37',
dest='build',
action='store',
help="Genome build (GRCh37 or GRCh38)")
parser.add_option('--mapping',
default='ncbi',
dest='mapping',
action='store',
help='Mapping source (ncbi or ucsc)')
parser.add_option('--output',
default='output',
dest='output',
action='store',
help='Output file name prefix')
(options, args) = parser.parse_args()
welcome('RefSeqDB')
toplevel.run(options)
goodbye('RefSeqDB')
def start_cli():
if len(sys.argv) == 1:
print '\nUsage: skeleton <project-name>\n'
quit()
toplevel.run(sys.argv[1])
def start_cli():
parser = OptionParser(description='SelectENSTs v{}'.format(__version__),
usage='CARTtools/selectensts <options>',
version=__version__)
parser.add_option('--mapped_nms',
default=None,
dest='mapped_nms',
action='store',
help="Mapped NMs data file (output of MapMMs)")
parser.add_option('--ensembl_data',
default=None,
dest='ensembl_data',
action='store',
help="Ensembl data file (output of EnsemblDB)")
parser.add_option('--gene_synonyms',
default=None,
dest='gene_synonyms',
action='store',
help="Gene synonyms file")
parser.add_option('--any_gene',
default=False,
dest='any_gene',
action='store_true',
help="Match a mapped NM to ENSTs with any gene symbol")
parser.add_option('--input',
default=None,
dest='input',
action='store',
help="Input file (list of NMs)")
parser.add_option('--output',
default=None,
dest='output',
action='store',
help="Output file name prefix")
(options, args) = parser.parse_args()
welcome('SelectENSTs')
toplevel.run(options)
goodbye('SelectENSTs')
def start_cli():
parser = OptionParser(description='[Project] v{}'.format(__version__),
usage='[Project]/[project] <options>',
version=__version__)
parser.add_option('-i',
'--input',
default=None,
dest='input',
action='store',
help="Input file")
(options, args) = parser.parse_args()
toplevel.run(options)
def start_cli():
parser = OptionParser(
description='CART_pipeline v{}'.format(__version__),
usage='CARTtools/cart_pipeline <options>',
version=__version__
)
parser.add_option(
'--config',
default=None,
dest='config',
action='store',
help="Configuration file"
)
(options, args) = parser.parse_args()
toplevel.run(options)
def start_cli():
parser = OptionParser(description='DeNovoFilter v{}'.format(__version__),
usage='DeNovoFilter/denovo <options>',
version=__version__)
parser.add_option('--child_var',
default=None,
dest='child_var',
action='store',
help='Variants data file of the child')
parser.add_option('--mother_var',
default=None,
dest='mother_var',
action='store',
help='Variants data file of the mother')
parser.add_option('--father_var',
default=None,
dest='father_var',
action='store',
help='Variants data file of the father')
parser.add_option('--child_bam',
default=None,
dest='child_bam',
action='store',
help='BAM file of the child')
parser.add_option('--mother_bam',
default=None,
dest='mother_bam',
action='store',
help='BAM file of the mother')
parser.add_option('--father_bam',
default=None,
dest='father_bam',
action='store',
help='BAM file of the father')
parser.add_option('--config',
default=None,
dest='config',
action='store',
help='Configuration file')
parser.add_option('--full_details',
default=False,
dest='full_details',
action='store_true',
help='Output full details')
parser.add_option('--output',
default=None,
dest='output',
action='store',
help='Output filename prefix')
(options, args) = parser.parse_args()
toplevel.run(options)
def start_cli():
parser = OptionParser(description='FormatCARTs v{}'.format(__version__),
usage='CARTtools/formatcarts <options>',
version=__version__)
parser.add_option('--selected_nms',
dest='selected_nms',
action='store',
help="Final selected NMs file (output of SelectNMs)")
parser.add_option('--selected_ensts',
dest='selected_ensts',
action='store',
help="Selected ENSTs file (output of SelectENSTs)")
parser.add_option('--canonical',
dest='canonical',
action='store',
help="Canonical ENSTs file")
parser.add_option('--ensembl',
default=None,
dest='ensembl',
action='store',
help="Ensembl transcript database (output of EnsemblDB)")
parser.add_option('--series',
default=None,
dest='series',
action='store',
help="CARTs series code (e.g. CART37A)")
parser.add_option('--output',
default='output',
dest='output',
action='store',
help="Output file name prefix")
parser.add_option('--gbk',
default=False,
dest='gbk',
action='store_true',
help="Create GBK output")
parser.add_option('--ref',
default=None,
dest='ref',
action='store',
help="Reference genome file")
parser.add_option('--annovar',
default=False,
dest='annovar',
action='store_true',
help="Create GenePred and FASTA files for Annovar")
parser.add_option(
'--prev_cava_db',
default=None,
dest='prev_cava_db',
action='store',
help=
"CAVA db output of previous run from which CART numbering will be continued"
)
parser.add_option(
'--prev_ref',
default=None,
dest='prev_ref',
action='store',
help=
"Reference genome of previous run from which CART numbering will be continued"
)
(options, args) = parser.parse_args()
welcome('FormatCARTs')
toplevel.run(options)
goodbye('FormatCARTs')
def start_cli():
parser = OptionParser(
description='MapNMs v{}'.format(__version__),
usage='CARTtools/mapnms <options>',
version=__version__
)
parser.add_option(
'--input',
default=None,
dest='input',
action='store',
help="Input file (output of SelectNMs)"
)
parser.add_option(
'--ncbi',
default=None,
dest='ncbi',
action='store',
help="RefSeqDB output file with NCBI interim mapping data"
)
parser.add_option(
'--ucsc',
default=None,
dest='ucsc',
action='store',
help="RefSeqDB output file with UCSC mapping data"
)
parser.add_option(
'--hgncid_to_symbol',
default=None,
dest='hgnc',
action='store',
help="HGNC ID to Gene Symbol dictionary file"
)
parser.add_option(
'--output',
default='output',
dest='output',
action='store',
help="Output file name prefix"
)
parser.add_option(
'--more_symbols',
default=None,
dest='symbols',
action='store',
help="TXT file for specifying gene symbols for missing HGNC IDs"
)
(options, args) = parser.parse_args()
welcome('MapNMs')
toplevel.run(options)
goodbye('MapNMs')
def start_cli():
parser = OptionParser(
description='SelectNMs v{}'.format(__version__),
usage='CARTtools/selectnms <options>',
version=__version__
)
parser.add_option(
'--input_genes',
default=None,
dest='hgnc',
action='store',
help="Input file containing HGNC IDs"
)
parser.add_option(
'--appris',
default=None,
dest='appr',
action='store',
help="APPRIS data file"
)
parser.add_option(
'--refsdb',
default=None,
dest='refsdb',
action='store',
help="RefSeq transcript database file (output of RefSeqDB)"
)
parser.add_option(
'--refschk',
default=None,
dest='refss',
action='store',
help="RefSeqCheck output file"
)
parser.add_option(
'--genes_dict',
default=None,
dest='genes',
action='store',
help="Gene ID dictionary file"
)
parser.add_option(
'--build',
default=None,
dest='build',
action='store',
help="Genome build (GRCh37 or GRCh38)"
)
parser.add_option(
'--out_auto',
dest='out',
action='store',
help="Output file name prefix for automatic selection"
)
parser.add_option(
'--out',
dest='out_final',
action='store',
help="Output file name prefix for final selection"
)
parser.add_option(
'--refsdbinc',
dest='refsdbinc',
action='store',
help="List of transcripts included in the RefSeq DB (output of RefSeqDB)"
)
(options, args) = parser.parse_args()
welcome('SelectNMs')
toplevel.run(options)
goodbye('SelectNMs')
def start_cli():
parser = OptionParser(
description='enstwriter v{}'.format(__version__),
usage='enstwriter <options>',
version=__version__
)
parser.add_option(
'--input',
default='input',
dest='input',
action='store',
help="Input file name [default value: %default]"
)
parser.add_option(
'--ensembl',
default=None,
dest='ensembl',
action='store',
help="Ensembl transcript database"
)
parser.add_option(
'--series',
default=None,
dest='series',
action='store',
help="Series code (e.g. CART37A)"
)
parser.add_option(
'--output',
default='output',
dest='output',
action='store',
help="Output file name prefix [default value: %default]"
)
parser.add_option(
'--gbk',
default=False,
dest='gbk',
action='store_true',
help="Create GBK output [default value: %default]"
)
parser.add_option(
'--ref',
default=None,
dest='ref',
action='store',
help="Reference genome file"
)
parser.add_option(
'--annovar',
default=False,
dest='annovar',
action='store_true',
help="Create GenePred and FASTA files for Annovar [default value: %default]"
)
parser.add_option(
'--prev_cava_db',
default=None,
dest='prev_cava_db',
action='store',
help="CAVA db output of previous run from which CART numbering will be continued"
)
parser.add_option(
'--prev_ref',
default=None,
dest='prev_ref',
action='store',
help="Reference genome of previous run from which CART numbering will be continued"
)
(options, args) = parser.parse_args()
toplevel.run(options)
def start_cli():
parser = OptionParser(
description='Summarize v{}'.format(__version__),
usage='CARTtools/summarize <options>',
version=__version__
)
parser.add_option(
'--prefix',
default=None,
dest='prefix',
action='store',
help="Input file prefix"
)
parser.add_option(
'--start',
default=None,
dest='start',
action='store',
help="Start date/time"
)
parser.add_option(
'--end',
default=None,
dest='end',
action='store',
help="End date/time"
)
parser.add_option(
'--inputfn',
default=None,
dest='inputfn',
action='store',
help="Gene input file name used in the pipeline"
)
parser.add_option(
'--configfn',
default=None,
dest='configfn',
action='store',
help="Config file name used in the pipeline"
)
parser.add_option(
'--ens37',
default=None,
dest='ens37',
action='store',
help="Ensembl transcript database (GRCh37)"
)
parser.add_option(
'--ens38',
default=None,
dest='ens38',
action='store',
help="Ensembl transcript database (GRCh38)"
)
parser.add_option(
'--output',
default=None,
dest='output',
action='store',
help="Output file name prefix"
)
(options, args) = parser.parse_args()
welcome('Summarize')
toplevel.run(options)
goodbye('Summarize')
def start_cli():
parser = OptionParser(description='CompareENSTs v{}'.format(__version__),
usage='CARTtools/compareensts <options>',
version=__version__)
parser.add_option('--input',
default=None,
dest='input',
action='store',
help="Input file")
parser.add_option(
'--ensts37',
default=None,
dest='enstsx',
action='store',
help="Table of selected ENSTs for GRCh37 (output of SelectedENSTs)")
parser.add_option(
'--ensts38',
default=None,
dest='enstsy',
action='store',
help="Table of selected ENSTs for GRCh38 (output of SelectedENSTs)")
parser.add_option('--data37',
default=None,
dest='dataX',
action='store',
help="Ensembl database for GRCh37 (output of EnsemblDB)")
parser.add_option('--data38',
default=None,
dest='dataY',
action='store',
help="Ensembl database for GRCh38 (output of EnsemblDB)")
parser.add_option('--ref37',
default=None,
dest='ref37',
action='store',
help="Reference genome fasta file (GRCh37)")
parser.add_option('--ref38',
default=None,
dest='ref38',
action='store',
help="Reference genome fasta file (GRCh38)")
parser.add_option('--output',
default=None,
dest='output',
action='store',
help="Output file name")
parser.add_option(
'--discr',
default=False,
dest='discr',
action='store_true',
help="Output only ENST pairs where there are differences")
parser.add_option('--simple',
default=False,
dest='simple',
action='store_true',
help="Create simplified output")
(options, args) = parser.parse_args()
welcome('CompareENSTs')
toplevel.run(options)
goodbye('CompareENSTs')
