changeset 30:b8271b9a1049 draft

planemo upload commit c89c5deac442c0c2aa52b24f2c5af4b290773fc0-dirty

--- a/data_manager/resource_building.py	Mon Jan 28 05:16:55 2019 -0500
+++ b/data_manager/resource_building.py	Mon Jan 28 08:14:27 2019 -0500
@@ -67,24 +67,29 @@
     sample_category_id = tissue[0]
     name = tissue[1]
     output_file = name+"_"+time.strftime("%d-%m-%Y") + ".tsv"
-    query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+sample_category_id+ \
-        "&display_options=ShowAbundances&organism_id="+organism_id+"&redundancy_constraint=4&presence_level_constraint=1%2C2"+ \ 
-        "&gene_annotation_level_constraint=leaf&QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"
-    download = requests.get(query)
-    decoded_content = download.content.decode('utf-8')
-    cr = csv.reader(decoded_content.splitlines(), delimiter='\t')
+
+    query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+ \
+    sample_category_id+"&display_options=ShowAbundances&organism_id="+organism_id+ \
+    "&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf\
+    &QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"
 
-    #build dictionary by only keeping uniprot accession (not isoform) as key and sum of observations as value
+    print (query)
+
+    with requests.Session() as s:
+        download = s.get(query)
+        decoded_content = download.content.decode('utf-8')
+        cr = csv.reader(decoded_content.splitlines(), delimiter='\t')
+        #cr = list(cr)
+
     uni_dict = build_dictionary(cr)
 
     #columns of data table peptide_atlas
     date = time.strftime("%d-%m-%Y")
-    tissue = tissue.split("-")[1]
-    tissue_id = tissue+"_"+date
+    tissue_id = name+"_"+date
     tissue_name = tissue_id.replace("-","/").replace("_"," ")
-    path = os.path.join(target_directory,output_file)
+    path = os.path.join(output_file)
 
-    with open(path,"wb") as out :
+    with open(path,"w") as out :
         w = csv.writer(out,delimiter='\t')
         w.writerow(["Uniprot_AC","nb_obs"])
         w.writerows(uni_dict.items())
@@ -96,11 +101,11 @@
 def build_dictionary (csv) :
     uni_dict = {} 
     for line in csv :
-        if "-" not in line[2] and check_uniprot_access(line[2]) :
-            if line[2] in uni_dict :
-                uni_dict[line[2]] += int(line[4])
+        if "-" not in line[0] and check_uniprot_access(line[0]) :
+            if line[0] in uni_dict :
+                uni_dict[line[0]] += int(line[5])
             else : 
-                uni_dict[line[2]] = int(line[4])
+                uni_dict[line[0]] = int(line[5])
 
     return uni_dict
 
@@ -112,8 +117,6 @@
     else :
         return False
 
-
-
 #######################################################################################################
 # 3. ID mapping file
 #######################################################################################################

--- a/data_manager/resource_building.xml	Mon Jan 28 05:16:55 2019 -0500
+++ b/data_manager/resource_building.xml	Mon Jan 28 08:14:27 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.25" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.01.25.1" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>