Mercurial > repos > jjohnson > data_manager_snpeff
comparison data_manager/data_manager_snpEff_download.py @ 3:c6769a700e55
Update loc data to separate version 4 databases
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Tue, 21 Oct 2014 14:04:33 -0500 |
| parents | bc50aa3b328a |
| children | 78bcf4ac437c |
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| 2:5a01e5cfa6bc | 3:c6769a700e55 |
|---|---|
| 108 for fname in files: | 108 for fname in files: |
| 109 if fname.startswith('snpEffectPredictor'): | 109 if fname.startswith('snpEffectPredictor'): |
| 110 # if snpEffectPredictor.bin download succeeded | 110 # if snpEffectPredictor.bin download succeeded |
| 111 name = genome_version + (' : ' + organism if organism else '') | 111 name = genome_version + (' : ' + organism if organism else '') |
| 112 data_table_entry = dict(value=genome_version, name=name, path=data_dir) | 112 data_table_entry = dict(value=genome_version, name=name, path=data_dir) |
| 113 _add_data_table_entry( data_manager_dict, 'snpeff_genomedb', data_table_entry ) | 113 _add_data_table_entry( data_manager_dict, 'snpeff4_genomedb', data_table_entry ) |
| 114 else: | 114 else: |
| 115 m = re.match(regulation_pattern,fname) | 115 m = re.match(regulation_pattern,fname) |
| 116 if m: | 116 if m: |
| 117 name = m.groups()[0] | 117 name = m.groups()[0] |
| 118 data_table_entry = dict(genome=genome_version,value=name, name=name) | 118 data_table_entry = dict(genome=genome_version,value=name, name=name) |
| 119 _add_data_table_entry( data_manager_dict, 'snpeff_regulationdb', data_table_entry ) | 119 _add_data_table_entry( data_manager_dict, 'snpeff4_regulationdb', data_table_entry ) |
| 120 elif fname in annotations_dict: | 120 elif fname in annotations_dict: |
| 121 value = annotations_dict[fname] | 121 value = annotations_dict[fname] |
| 122 name = value.lstrip('-') | 122 name = value.lstrip('-') |
| 123 data_table_entry = dict(genome=genome_version,value=value, name=name) | 123 data_table_entry = dict(genome=genome_version,value=value, name=name) |
| 124 _add_data_table_entry( data_manager_dict, 'snpeff_annotations', data_table_entry ) | 124 _add_data_table_entry( data_manager_dict, 'snpeff4_annotations', data_table_entry ) |
| 125 return data_manager_dict | 125 return data_manager_dict |
| 126 | 126 |
| 127 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ): | 127 def _add_data_table_entry( data_manager_dict, data_table, data_table_entry ): |
| 128 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) | 128 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) |
| 129 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) | 129 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] ) |