Mercurial > repos > greg > extract_genomic_dna
comparison extract_genomic_dna.py @ 3:c46db4f7c869 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 14 Jan 2016 09:38:50 -0500 |
| parents | 311febbd33d6 |
| children | 6333e08869fc |
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| 2:cc1879e0b0ae | 3:c46db4f7c869 |
|---|---|
| 64 def stop_err(msg): | 64 def stop_err(msg): |
| 65 sys.stderr.write(msg) | 65 sys.stderr.write(msg) |
| 66 sys.exit(1) | 66 sys.exit(1) |
| 67 | 67 |
| 68 parser = argparse.ArgumentParser() | 68 parser = argparse.ArgumentParser() |
| 69 parser.add_option('--input_format', dest='input_format', help="Input dataset format") | 69 parser.add_argument('--input_format', dest='input_format', help="Input dataset format") |
| 70 parser.add_option('--input', dest='input', help="Input dataset") | 70 parser.add_argument('--input', dest='input', help="Input dataset") |
| 71 parser.add_option('--genome', dest='genome', help="Input dataset genome build") | 71 parser.add_argument('--genome', dest='genome', help="Input dataset genome build") |
| 72 parser.add_option('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff") | 72 parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff") |
| 73 parser.add_option('--columns', dest='columns', help="Columns to use in input file") | 73 parser.add_argument('--columns', dest='columns', help="Columns to use in input file") |
| 74 parser.add_option('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file") | 74 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file") |
| 75 parser.add_option('--reference_genome', dest='reference_genome', help="Reference genome file") | 75 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file") |
| 76 parser.add_option('--output_format', dest='output_format', help="Output format") | 76 parser.add_argument('--output_format', dest='output_format', help="Output format") |
| 77 parser.add_option('--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.cols.split(',')) == 5: |