Mercurial > repos > sanbi-uwc > data_manager_novocraft_index_builder
comparison data_manager/novocraft_index_builder.py @ 12:283eec05d1de draft
planemo upload for repository https://github.com/zipho/data_manager_novocraft_index_builder commit e14dbfe322e3787d1ec9b7467a3677b101784227
| author | sanbi-uwc |
|---|---|
| date | Tue, 08 Mar 2016 05:38:52 -0500 |
| parents | a9b725202132 |
| children | d053e7b179b5 |
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| 11:a9b725202132 | 12:283eec05d1de |
|---|---|
| 35 print("Output directory path already exists but is not a directory: {}".format(target_directory), | 35 print("Output directory path already exists but is not a directory: {}".format(target_directory), |
| 36 file=sys.stderr) | 36 file=sys.stderr) |
| 37 elif not os.path.exists(target_directory): | 37 elif not os.path.exists(target_directory): |
| 38 os.mkdir(target_directory) | 38 os.mkdir(target_directory) |
| 39 | 39 |
| 40 index_filename = os.path.join(target_directory,"%.nix" % sequence_id) | 40 print(sequence_id) |
| 41 nix_file = sequence_id + ".nix" | |
| 42 index_filename = os.path.join(target_directory, nix_file) | |
| 41 cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename) | 43 cmdline_str = 'novoindex {} {}'.format(index_filename, fasta_filename) |
| 42 cmdline = shlex.split(cmdline_str) | 44 cmdline = shlex.split(cmdline_str) |
| 43 | 45 |
| 44 #index_filename = 'foo' | |
| 45 #cmdline = ('touch', '{}/{}'.format(target_directory, index_filename)) | |
| 46 try: | 46 try: |
| 47 print(cmdline) | |
| 47 check_call(cmdline) | 48 check_call(cmdline) |
| 48 except CalledProcessError: | 49 except CalledProcessError: |
| 49 print("Error building RNA STAR index", file=sys.stderr) | 50 print("Error building RNA STAR index", file=sys.stderr) |
| 50 | 51 |
| 51 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=index_filename ) | 52 data_table_entry = dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=index_filename ) |
| 81 | 82 |
| 82 filename = args.output_filename | 83 filename = args.output_filename |
| 83 | 84 |
| 84 params = loads(open(filename).read()) | 85 params = loads(open(filename).read()) |
| 85 target_directory = params['output_data'][0]['extra_files_path'] | 86 target_directory = params['output_data'][0]['extra_files_path'] |
| 86 os.makedirs(target_directory) | 87 #os.makedirs(target_directory) |
| 87 data_manager_dict = {} | 88 data_manager_dict = {} |
| 88 | 89 |
| 89 dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description) | 90 dbkey, sequence_id, sequence_name = get_dbkey_id_name(params, dbkey_description=args.dbkey_description) |
| 90 | 91 |
| 91 if dbkey in [None, '', '?']: | 92 if dbkey in [None, '', '?']: |