Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.py @ 14:1a10864abc1f draft

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author greg
date Wed, 02 Mar 2016 09:13:24 -0500
parents 8cc00c5cf33e
children e70f5ca82b63
comparison
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13:fe88f4eeaddc 14:1a10864abc1f
15 parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff") 15 parser.add_argument('--interpret_features', dest='interpret_features', default=None, help="Interpret features if input format is gff")
16 parser.add_argument('--columns', dest='columns', help="Columns to use in input file") 16 parser.add_argument('--columns', dest='columns', help="Columns to use in input file")
17 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file") 17 parser.add_argument('--reference_genome_source', dest='reference_genome_source', help="Source of reference genome file")
18 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file") 18 parser.add_argument('--reference_genome', dest='reference_genome', help="Reference genome file")
19 parser.add_argument('--output_format', dest='output_format', help="Output format") 19 parser.add_argument('--output_format', dest='output_format', help="Output format")
20 parser.add_argument('--description_field_delimiter', dest='description_field_delimiter', default=None, help="Fasta description field delimiter")
20 parser.add_argument('--output', dest='output', help="Output dataset") 21 parser.add_argument('--output', dest='output', help="Output dataset")
21 args = parser.parse_args() 22 args = parser.parse_args()
22 23
23 input_is_gff = args.input_format == 'gff' 24 input_is_gff = args.input_format == 'gff'
24 interpret_features = input_is_gff and args.interpret_features == "yes" 25 interpret_features = input_is_gff and args.interpret_features == "yes"
157 l = len(sequence) 158 l = len(sequence)
158 c = 0 159 c = 0
159 if input_is_gff: 160 if input_is_gff:
160 start, end = egdu.convert_bed_coords_to_gff([start, end]) 161 start, end = egdu.convert_bed_coords_to_gff([start, end])
161 fields = [args.genome, str(chrom), str(start), str(end), strand] 162 fields = [args.genome, str(chrom), str(start), str(end), strand]
162 meta_data = "_".join(fields) 163 field_delimiter = extract_genomic_dna_utils.get_description_field_delimiter(args.description_field_delimiter)
164 meta_data = field_delimiter.join(fields)
163 if name.strip(): 165 if name.strip():
164 out.write(">%s %s\n" % (meta_data, name)) 166 out.write(">%s %s\n" % (meta_data, name))
165 else: 167 else:
166 out.write(">%s\n" % meta_data) 168 out.write(">%s\n" % meta_data)
167 while c < l: 169 while c < l: