Mercurial > repos > greg > fasta_extract

comparison fasta_extract.py @ 4:99c868b492bb draft

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Uploaded
author greg
date Sun, 10 Jan 2016 14:01:04 -0500
parents 79167132946d
children 24769b1ca957
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3:79167132946d 4:99c868b492bb
40 args = parser.parse_args() 40 args = parser.parse_args()
41 41
42 fasta = Fasta(args.genome_file) 42 fasta = Fasta(args.genome_file)
43 43
44 for (input_filename, hid) in args.inputs: 44 for (input_filename, hid) in args.inputs:
45 hid = int(hid)
45 extend_existing = args.extend_existing == 'existing' 46 extend_existing = args.extend_existing == 'existing'
46 consider_strand = args.strand == 'yes' 47 consider_strand = args.strand == 'yes'
47 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t') 48 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t')
48 fasta_output_path = get_output_path(hid, 49 fasta_output_path = get_output_path(hid,
49 args.subtract_from_start, 50 args.subtract_from_start,