Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 22:4296fb613d9d draft

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planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty
author proteore
date Tue, 07 May 2019 10:29:13 -0400
parents 026177e4ff4b
children ebdd4961c6c2
comparison
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21:026177e4ff4b 22:4296fb613d9d
150 os.remove(tab_path) 150 os.remove(tab_path)
151 151
152 #print("selected_tab ok") 152 #print("selected_tab ok")
153 153
154 #get uniprot-AC reviewed 154 #get uniprot-AC reviewed
155 query = "https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:"+species_dict[species]+"&format=list" 155 organism = species_dict[species].split("_")[1]
156 query = "https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:"+organism+"&format=list"
156 157
157 with requests.Session() as s: 158 with requests.Session() as s:
158 download = s.get(query) 159 download = s.get(query)
159 decoded_content = download.content.decode('utf-8') 160 decoded_content = download.content.decode('utf-8')
160 uniprot_reviewed_list = decoded_content.splitlines() 161 uniprot_reviewed_list = decoded_content.splitlines()