Mercurial > repos > greg > fasta_extract

comparison fasta_extract.py @ 10:a3f52920020b draft

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Uploaded
author greg
date Sun, 10 Jan 2016 14:39:51 -0500
parents 4f6eba6beef5
children 48f6e9f1c19d
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9:67171d711b34 10:a3f52920020b
42 args = parser.parse_args() 42 args = parser.parse_args()
43 43
44 fasta = Fasta(args.genome_file) 44 fasta = Fasta(args.genome_file)
45 45
46 for (input_filename, hid) in args.inputs: 46 for (input_filename, hid) in args.inputs:
47 hid = int(hid)
47 extend_existing = args.extend_existing == 'existing' 48 extend_existing = args.extend_existing == 'existing'
48 consider_strand = args.strand == 'yes' 49 consider_strand = args.strand == 'yes'
49 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t') 50 reader = csv.reader(open(input_filename, 'rU'), delimiter='\t')
50 fasta_output_path = get_output_path(hid, 51 fasta_output_path = get_output_path(hid,
51 args.subtract_from_start, 52 args.subtract_from_start,