Mercurial > repos > proteore > proteore_data_manager
diff data_manager/resource_building.py @ 1:0915249b8c4b draft
planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty
| author | proteore |
|---|---|
| date | Wed, 06 Mar 2019 08:53:06 -0500 |
| parents | 0a26460d7366 |
| children | 2e34ee6d2d37 |
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--- a/data_manager/resource_building.py Mon Mar 04 05:03:04 2019 -0500 +++ b/data_manager/resource_building.py Wed Mar 06 08:53:06 2019 -0500 @@ -39,12 +39,15 @@ if tissue == "HPA_normal_tissue": tissue_name = "HPA normal tissue" url = "https://www.proteinatlas.org/download/normal_tissue.tsv.zip" + table = "proteore_protein_atlas_normal_tissue" elif tissue == "HPA_pathology": tissue_name = "HPA pathology" url = "https://www.proteinatlas.org/download/pathology.tsv.zip" + table = "proteore_protein_atlas_tumor_tissue" elif tissue == "HPA_full_atlas": tissue_name = "HPA full atlas" url = "https://www.proteinatlas.org/download/proteinatlas.tsv.zip" + table = "proteore_protein_full_atlas" output_file = tissue +"_"+ time.strftime("%d-%m-%Y") + ".tsv" path = os.path.join(target_directory, output_file) @@ -52,8 +55,9 @@ tissue_name = tissue_name + " " + time.strftime("%d/%m/%Y") tissue_id = tissue_name.replace(" ","_").replace("/","-") + data_table_entry = dict(id=tissue_id, name = tissue_name, tissue = tissue, value = path) - _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_protein_atlas") + _add_data_table_entry(data_manager_dict, data_table_entry, table) ####################################################################################################### @@ -228,7 +232,7 @@ id = species+"_id_mapping_"+ time.strftime("%d-%m-%Y") data_table_entry = dict(id=id, name = name, value = species, path = path) - _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping") + _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_idmapping_"+species) def download_from_uniprot_ftp(file,target_directory) : ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
