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')