Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder
comparison data_manager/rnastar_index_builder.py @ 9:ccb7ce1ad9b3 draft
planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit fbd0bba2d1b19756849695e02e17d86076ca74a1
| author | sanbi-uwc |
|---|---|
| date | Fri, 12 Feb 2016 03:30:43 -0500 |
| parents | 56686a746b91 |
| children | 61084615bb57 |
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| 8:56686a746b91 | 9:ccb7ce1ad9b3 |
|---|---|
| 54 parser = argparse.ArgumentParser(description="Generate RNA STAR genome index and JSON describing this") | 54 parser = argparse.ArgumentParser(description="Generate RNA STAR genome index and JSON describing this") |
| 55 parser.add_argument('output_filename') | 55 parser.add_argument('output_filename') |
| 56 parser.add_argument('--fasta_filename') | 56 parser.add_argument('--fasta_filename') |
| 57 parser.add_argument('--fasta_dbkey') | 57 parser.add_argument('--fasta_dbkey') |
| 58 parser.add_argument('--fasta_description', default=None) | 58 parser.add_argument('--fasta_description', default=None) |
| 59 parser.add_argument('--data_table_name', default='rnastar_index') | 59 parser.add_argument('--data_table_name', default='rnastar_indexes') |
| 60 args = parser.parse_args() | 60 args = parser.parse_args() |
| 61 | 61 |
| 62 filename = args.output_filename | 62 filename = args.output_filename |
| 63 | 63 |
| 64 params = load(open(filename, 'rb')) | 64 params = load(open(filename, 'rb')) |
| 65 print(params) | |
| 65 output_directory = params[ 'output_data' ][0]['extra_files_path'] | 66 output_directory = params[ 'output_data' ][0]['extra_files_path'] |
| 66 makedirs( output_directory ) | 67 makedirs( output_directory ) |
| 67 data_manager_dict = {} | 68 data_manager_dict = {} |
| 68 | 69 |
| 69 make_rnastar_index(output_directory, args.fasta_filename) | 70 make_rnastar_index(output_directory, args.fasta_filename) |
| 70 (sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description) | 71 (sequence_id, sequence_name) = get_id_name(params, args.fasta_dbkey, args.fasta_description) |
| 71 data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory) | 72 data_table_entry = dict(value=sequence_id, dbkey=args.fasta_dbkey, name=sequence_name, path=output_directory) |
| 72 | 73 |
| 73 #dt_tables = {args.data_table_name : [data_table_entry]} | |
| 74 output_datatable_dict = dict(data_tables={args.data_table_name : [data_table_entry]}) | 74 output_datatable_dict = dict(data_tables={args.data_table_name : [data_table_entry]}) |
| 75 open( filename, 'wb' ).write( dumps( output_datatable_dict ) ) | 75 open( filename, 'wb' ).write( dumps( output_datatable_dict ) ) |