Mercurial > repos > greg > extract_genomic_dna

comparison extract_genomic_dna.py @ 5:ee00b3c68801 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 14 Jan 2016 10:43:42 -0500
parents 6333e08869fc
children 8cc00c5cf33e
comparison
equal deleted inserted replaced
4:6333e08869fc 5:ee00b3c68801
171 if not invalid_lines: 171 if not invalid_lines:
172 invalid_lines = get_lines(feature) 172 invalid_lines = get_lines(feature)
173 first_invalid_line = line_count 173 first_invalid_line = line_count
174 skipped_lines += len(invalid_lines) 174 skipped_lines += len(invalid_lines)
175 continue 175 continue
176 elif os.path.isfile(os.path.join(seq_dir, '%s.2bit' % args.genome)): 176 elif os.path.isfile(seq_path):
177 if not(twobitfile): 177 if not(twobitfile):
178 twobitfile = bx.seq.twobit.TwoBitFile(file(seq_path)) 178 twobitfile = bx.seq.twobit.TwoBitFile(file(seq_path))
179 try: 179 try:
180 if interpret_features: 180 if interpret_features:
181 # Create sequence from intervals within a feature. 181 # Create sequence from intervals within a feature.