Mercurial > repos > proteore > proteore_data_manager

changeset 40:a7bcc9a0a456 draft

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"planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty"
author proteore
date Wed, 08 Jan 2020 13:28:05 +0000
parents 45dc32d0afa0
children fe21769281fa
files data_manager/resource_building.py data_manager/resource_building.xml
diffstat 2 files changed, 6 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.py	Wed Jan 08 13:11:36 2020 +0000
+++ b/data_manager/resource_building.py	Wed Jan 08 13:28:05 2020 +0000
@@ -150,6 +150,7 @@
         tab_reader = csv.reader(select,delimiter="\t")
         for line in tab_reader :
             tab.append([line[0]]+[line[i] for i in [0,1,2,3,4,5,6,11,13,14,18,19,20]])
+    if os.path.exists(os.path.join(archive,tab_path[-1])) : os.remove(os.path.join(archive,tab_path[-1]))
     shutil.move(tab_path, archive)
     #print("selected_tab ok")
 
@@ -185,7 +186,7 @@
     unidict = {}
 
     #keep only ids of interest in dictionaries
-    dat_file=species_dict[species]+"_"+files[1]
+    dat_file = species_dict[species]+"_"+files[1]
     dat_path = download_from_uniprot_ftp(dat_file,target_directory)
     with gzip.open(dat_path,"rt") as dat :
         dat_reader = csv.reader(dat,delimiter="\t")
@@ -201,6 +202,7 @@
                         unidict[uniprotID].update({ id_type : cor_id })
                 elif  id_type in ids :
                     unidict[uniprotID]={id_type : cor_id}
+    if os.path.exists(os.path.join(archive,dat_path[-1])) : os.remove(os.path.join(archive,dat_path[-1]))
     shutil.move(dat_path, archive)
 
     #print("dat_file ok")
@@ -231,6 +233,7 @@
         nextprot_path = id_list_from_nextprot_ftp("nextprot_ac_list_all.txt",target_directory)
         with open(nextprot_path,'r') as nextprot_ids :
             nextprot_ids = nextprot_ids.read().splitlines()
+        if os.path.exists(os.path.join(archive,nextprot_path[-1])) : os.remove(os.path.join(archive,nextprot_path[-1]))
         shutil.move(nextprot_path,archive)
         next_dict = {}
         for nextid in nextprot_ids : 
@@ -644,7 +647,7 @@
 
     ## Download ID_mapping source file from Uniprot
     try:
-        id_mapping=args.id_mapping
+        id_mapping = args.id_mapping
     except NameError:
         id_mapping = None
     if id_mapping is not None:
--- a/data_manager/resource_building.xml	Wed Jan 08 13:11:36 2020 +0000
+++ b/data_manager/resource_building.xml	Wed Jan 08 13:28:05 2020 +0000
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.08.8" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2020.01.08.9" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>