Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.py @ 4:6333e08869fc draft

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Uploaded
author greg
date Thu, 14 Jan 2016 09:40:51 -0500
parents c46db4f7c869
children ee00b3c68801
comparison
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3:c46db4f7c869 4:6333e08869fc
77 parser.add_argument('--output', dest='output', help="Output dataset") 77 parser.add_argument('--output', dest='output', help="Output dataset")
78 args = parser.parse_args() 78 args = parser.parse_args()
79 79
80 input_is_gff = args.input_format == 'gff' 80 input_is_gff = args.input_format == 'gff'
81 interpret_features = input_is_gff and args.interpret_features == "yes" 81 interpret_features = input_is_gff and args.interpret_features == "yes"
82 if len(args.cols.split(',')) == 5: 82 if len(args.columns.split(',')) == 5:
83 # Bed file. 83 # Bed file.
84 chrom_col, start_col, end_col, strand_col, name_col = parse_cols_arg(args.cols) 84 chrom_col, start_col, end_col, strand_col, name_col = parse_cols_arg(args.columns)
85 else: 85 else:
86 # Gff file. 86 # Gff file.
87 chrom_col, start_col, end_col, strand_col = parse_cols_arg(args.cols) 87 chrom_col, start_col, end_col, strand_col = parse_cols_arg(args.columns)
88 name_col = False 88 name_col = False
89 89
90 if args.reference_genome_source == "history": 90 if args.reference_genome_source == "history":
91 seq_path = convert_to_twobit(args.reference_genome) 91 seq_path = convert_to_twobit(args.reference_genome)
92 else: 92 else: