Mercurial > repos > ieguinoa > data_manager_salmon_index_builder

comparison data_manager/salmon_index_builder.py @ 8:cbe62bd6e149 draft

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author ieguinoa
date Tue, 23 Jul 2019 11:12:15 -0400
parents d22f69a2e80e
children
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7:954d617c323d 8:cbe62bd6e149
57 parser.add_argument( '--output', dest='output', action='store', type=str, default=None ) 57 parser.add_argument( '--output', dest='output', action='store', type=str, default=None )
58 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None ) 58 parser.add_argument( '--fasta_filename', dest='fasta_filename', action='store', type=str, default=None )
59 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None ) 59 parser.add_argument( '--fasta_dbkey', dest='fasta_dbkey', action='store', type=str, default=None )
60 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None ) 60 parser.add_argument( '--fasta_description', dest='fasta_description', action='store', type=str, default=None )
61 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes' ) 61 parser.add_argument( '--data_table_name', dest='data_table_name', action='store', type=str, default='salmon_indexes' )
62 parser.add_argument( '-v','--index_version', dest='index_version', action='store', type=str, help='Use IndexVersion attribute from header.json' )
62 parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' ) 63 parser.add_argument( '-k', '--kmer_size', dest='kmer_size', action='store', type=str, help='kmer_size' )
63 options = parser.parse_args() 64 options = parser.parse_args()
64 65
65 filename = options.output 66 filename = options.output
66 67