add_argument( 'db', help = 'Database to download. For srst2_argannot: default is latest version r2, use r1 to get the older version') For plasmid/res/virulencefinder: default is to get latest from bitbucket - supply git commit hash to get a specific version from bitbucket, or use "old " to get from old website. Applies to: card, megares, ncbi, plasmidfinder, resfinder, srst2_argannot, virulencefinder. add_argument( '-version', help = 'Version of reference data to download. add_argument( '-debug', action = 'store_true', help = 'Do not delete temporary downloaded files') add_parser(ĭescription = 'Download reference data from one of a few supported public resources',
#- getref -Īllowed_dbs = sorted( list( ariba. add_argument( 'flag_in', type = int, help = 'Flag to be translated (an integer)', metavar = 'flag') Help = 'Expands flag column of report file',ĭescription = 'Translate the meaning of a flag output by ARIBA, found in the report tsv file', add_argument( 'outprefix', help = 'Prefix of output filenames') join( coding_choices), choices = coding_choices, metavar = '(non)coding') add_argument( 'coding_or_non', help = 'Sequences are coding or noncoding. add_argument( 'variants_tsv', help = 'TSV file of variants information') add_argument( 'aln_fasta', help = 'Multi-fasta file of alignments') By default they are considered to be presence/absence')
add_argument( '-variant_only', action = 'store_true', help = 'Use this to flag all sequences as variant only. Currently supported 1,4,11 ', choices =, default = 11, metavar = 'INT') add_argument( '-genetic_code', type = int, help = 'Number of genetic code to use. Help = 'Converts multi-aln fasta and SNPs to metadata',ĭescription = 'Make metadata input to prepareref, using multialignment and SNPs', add_subparsers( title = 'Available commands', help = '', metavar = '')
Description = 'ARIBA: Antibiotic Resistance Identification By Assembly',
0 kommentar(er)
