Mercurial > repos > greg > fasta_extract
comparison fasta_extract.py @ 3:79167132946d draft
Uploaded
| author | greg |
|---|---|
| date | Sun, 10 Jan 2016 13:56:47 -0500 |
| parents | 3fb7f36c2c8a |
| children | 99c868b492bb |
comparison
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| 2:4dc6890db112 | 3:79167132946d |
|---|---|
| 43 | 43 |
| 44 for (input_filename, hid) in args.inputs: | 44 for (input_filename, hid) in args.inputs: |
| 45 extend_existing = args.extend_existing == 'existing' | 45 extend_existing = args.extend_existing == 'existing' |
| 46 consider_strand = args.strand == 'yes' | 46 consider_strand = args.strand == 'yes' |
| 47 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t') | 47 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t') |
| 48 fasta_output_path = get_output_path(args.hid, | 48 fasta_output_path = get_output_path(hid, |
| 49 args.subtract_from_start, | 49 args.subtract_from_start, |
| 50 args.add_to_end, | 50 args.add_to_end, |
| 51 extend_existing, | 51 extend_existing, |
| 52 consider_strand) | 52 consider_strand) |
| 53 output = open(fasta_output_path, 'wb') | 53 output = open(fasta_output_path, 'wb') |
| 54 gff_output_path = get_output_path(args.hid, | 54 gff_output_path = get_output_path(hid, |
| 55 args.subtract_from_start, | 55 args.subtract_from_start, |
| 56 args.add_to_end, | 56 args.add_to_end, |
| 57 extend_existing, | 57 extend_existing, |
| 58 consider_strand, | 58 consider_strand, |
| 59 orphan=True) | 59 orphan=True) |