Mercurial > repos > proteore > proteore_data_manager

comparison data_manager/resource_building.py @ 37:807ecb8c3867 draft

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"planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty"
author proteore
date Wed, 08 Jan 2020 10:52:44 +0000
parents b18cb0d11971
children 6daab0a711e2
comparison
equal deleted inserted replaced
36:b18cb0d11971 37:807ecb8c3867
135 135
136 human = species == "Human" 136 human = species == "Human"
137 species_dict = { "Human" : "HUMAN_9606", "Mouse" : "MOUSE_10090", "Rat" : "RAT_10116" } 137 species_dict = { "Human" : "HUMAN_9606", "Mouse" : "MOUSE_10090", "Rat" : "RAT_10116" }
138 files=["idmapping_selected.tab.gz","idmapping.dat.gz"] 138 files=["idmapping_selected.tab.gz","idmapping.dat.gz"]
139 archive = os.path.join(tool_data_path, "id_mapping/ID_mapping_archive_"+species+"_"+str(time.strftime("%Y%m%d"))) 139 archive = os.path.join(tool_data_path, "id_mapping/ID_mapping_archive_"+species+"_"+str(time.strftime("%Y%m%d")))
140 if os.path.isfile is False : os.mkdir(archive) 140 if os.path.isfile(archive) is False : os.mkdir(archive)
141 141
142 #header 142 #header
143 if human : tab = [["UniProt-AC","UniProt-AC_reviewed","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","neXtProt","BioGrid","STRING","KEGG",'Gene_Name']] 143 if human : tab = [["UniProt-AC","UniProt-AC_reviewed","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","neXtProt","BioGrid","STRING","KEGG",'Gene_Name']]
144 else : tab = [["UniProt-AC","UniProt-AC_reviewed","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","BioGrid","STRING","KEGG",'Gene_Name']] 144 else : tab = [["UniProt-AC","UniProt-AC_reviewed","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","BioGrid","STRING","KEGG",'Gene_Name']]
145 145