Mercurial > repos > proteore > proteore_data_manager

changeset 28:808c8493ed4f draft

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planemo upload commit 5c2c274361c0daceae1f678eca0e6c0d5b4ba4f7-dirty
author proteore
date Mon, 27 May 2019 07:49:19 -0400
parents 9a400ce8e4e6
children 9a40b72414de
files data_manager/resource_building.py data_manager/resource_building.xml
diffstat 2 files changed, 5 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Fri May 17 04:09:47 2019 -0400
+++ b/data_manager/resource_building.py	Mon May 27 07:49:19 2019 -0400
@@ -138,8 +138,8 @@
     files=["idmapping_selected.tab.gz","idmapping.dat.gz"]
 
     #header
-    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"]]
-    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"]]
+    if human : tab = [["UniProt-AC","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","neXtProt","BioGrid","STRING","KEGG"]]
+    else : tab = [["UniProt-AC","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","BioGrid","STRING","KEGG"]]
 
     #get selected.tab and keep only ids of interest
     selected_tab_file=species_dict[species]+"_"+files[0]
@@ -163,10 +163,8 @@
 
     for line in tab[1:]:
         UniProtAC = line[0]
-        if UniProtAC in uniprot_reviewed_list :
-            line.insert(1,UniProtAC)
-        else : 
-            line.insert(1,"")
+        if UniProtAC not in uniprot_reviewed_list :
+            line[0]="NA"
 
     """
     Supplementary ID to get from HUMAN_9606_idmapping.dat :
--- a/data_manager/resource_building.xml	Fri May 17 04:09:47 2019 -0400
+++ b/data_manager/resource_building.xml	Mon May 27 07:49:19 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.05.17" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.05.27" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>