Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.py @ 15:e70f5ca82b63 draft

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Uploaded
author greg
date Wed, 02 Mar 2016 16:30:29 -0500
parents 1a10864abc1f
children 24c055f48065
comparison
equal deleted inserted replaced
14:1a10864abc1f 15:e70f5ca82b63
158 l = len(sequence) 158 l = len(sequence)
159 c = 0 159 c = 0
160 if input_is_gff: 160 if input_is_gff:
161 start, end = egdu.convert_bed_coords_to_gff([start, end]) 161 start, end = egdu.convert_bed_coords_to_gff([start, end])
162 fields = [args.genome, str(chrom), str(start), str(end), strand] 162 fields = [args.genome, str(chrom), str(start), str(end), strand]
163 field_delimiter = extract_genomic_dna_utils.get_description_field_delimiter(args.description_field_delimiter) 163 field_delimiter = egdu.get_description_field_delimiter(args.description_field_delimiter)
164 meta_data = field_delimiter.join(fields) 164 meta_data = field_delimiter.join(fields)
165 if name.strip(): 165 if name.strip():
166 out.write(">%s %s\n" % (meta_data, name)) 166 out.write(">%s %s\n" % (meta_data, name))
167 else: 167 else:
168 out.write(">%s\n" % meta_data) 168 out.write(">%s\n" % meta_data)