Mercurial > repos > proteore > proteore_data_manager
comparison data_manager/resource_building.py @ 32:ec1febc6672e draft
"planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty"
| author | proteore |
|---|---|
| date | Wed, 08 Jan 2020 10:04:51 +0000 |
| parents | faeeabb11a4d |
| children | e681d7de4f5e |
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| 31:faeeabb11a4d | 32:ec1febc6672e |
|---|---|
| 638 peptide_atlas = None | 638 peptide_atlas = None |
| 639 if peptide_atlas is not None: | 639 if peptide_atlas is not None: |
| 640 #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/" | 640 #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/" |
| 641 peptide_atlas = peptide_atlas.split(",") | 641 peptide_atlas = peptide_atlas.split(",") |
| 642 for pa_tissue in peptide_atlas: | 642 for pa_tissue in peptide_atlas: |
| 643 peptide_atlas_sources(data_manager_dict, pa_tissue, date, target_directory, args.tool_data_path) | 643 peptide_atlas_sources(data_manager_dict, pa_tissue, date, target_directory) |
| 644 | 644 |
| 645 ## Download ID_mapping source file from Uniprot | 645 ## Download ID_mapping source file from Uniprot |
| 646 try: | 646 try: |
| 647 id_mapping=args.id_mapping | 647 id_mapping=args.id_mapping |
| 648 except NameError: | 648 except NameError: |
| 649 id_mapping = None | 649 id_mapping = None |
| 650 if id_mapping is not None: | 650 if id_mapping is not None: |
| 651 id_mapping = id_mapping .split(",") | 651 id_mapping = id_mapping .split(",") |
| 652 for species in id_mapping : | 652 for species in id_mapping : |
| 653 id_mapping_sources(data_manager_dict, species, target_directory) | 653 id_mapping_sources(data_manager_dict, species, target_directory, args.tool_data_path)) |
| 654 | 654 |
| 655 ## Download PPI ref files from biogrid/bioplex/humap | 655 ## Download PPI ref files from biogrid/bioplex/humap |
| 656 try: | 656 try: |
| 657 interactome=args.interactome | 657 interactome=args.interactome |
| 658 if interactome == "biogrid" : | 658 if interactome == "biogrid" : |