fixed GN in mutations table of the DB

russelllab · May 5, 2023 · 3222121 · 3222121
1 parent 8ab14f8
commit 3222121
Show file tree

Hide file tree

Showing 3 changed files with 13 additions and 6 deletions.
diff --git a/DB/make_db.py b/DB/make_db.py
@@ -11,6 +11,8 @@
 import psycopg2
 # from backports import zoneinfo
 import pandas as pd
+sys.path.insert(1, '../ML/')
+import fetchData
 
 def connection():
     '''Function to connect to postgresql database'''
@@ -218,7 +220,8 @@ def fetch_mappings_dic():
 def find_pfampos(mycursor, acc, uniprotPos)->None:
     mycursor.execute("select pfampos from positions \
                      where acc=%s and uniprotpos=%s", (acc, uniprotPos))
-    pfamPos = mycursor.fetchone()[0]
+    pfamPos = mycursor.fetchone()
+    if pfamPos is not None: pfamPos = pfamPos[0]
     return pfamPos
 
 def create_mutations_table(mycursor)->None:
@@ -241,7 +244,9 @@ def create_mutations_table(mycursor)->None:
         mutAA = line.split('\t')[4].replace(',', '')
         if len(wtAA) > 1 or len(mutAA) > 1: continue
         wtPos = str(line.split('\t')[3])
+        print (gene, acc, wtAA, wtPos, mutAA)
         pfamPos = find_pfampos(mycursor, acc, wtPos)
+        if pfamPos is None: continue
         mut_type = line.split('\t')[5]
         # print (acc, kinases[acc].gene, wtAA, position, mutAA)
         mutation = wtAA + wtPos + mutAA
@@ -258,6 +263,7 @@ def create_mutations_table(mycursor)->None:
     for line in open('../AK_mut_w_sc_feb2023/res_mut_v3_only_subs_KD_neighb.tsv', 'r'):
         if line.split('\t')[0] == 'uniprot_id': continue
         acc = line.split('\t')[0]
+        acc, gene, uniprot_id, protein_name = fetchData.getAccGene(mycursor, acc)
         wtAA = line.split('\t')[1]
         mutAA = line.split('\t')[3]
         if mutAA == 'X': continue
@@ -280,6 +286,7 @@ def create_mutations_table(mycursor)->None:
     for line in open('../AK_mut_w_sc_feb2023/nat_mut_tidy_v2_march2023.tsv', 'r'):
         if line.split('\t')[1] == 'UniProtID': continue
         acc = line.split('\t')[1]
+        acc, gene, uniprot_id, protein_name = fetchData.getAccGene(mycursor, acc)
         wtAA = line.split('\t')[2]
         mutAA = line.split('\t')[4]
         if mutAA == 'X': continue
@@ -509,8 +516,8 @@ def create_kinases_table(mycursor)->None:
 
     # Create tables
     # create_hmm_table(mycursor)
-    create_kinases_table(mycursor)
-    # create_mutations_table(mycursor)
+    # create_kinases_table(mycursor)
+    create_mutations_table(mycursor)
     # create_homology_table(mycursor)
     # create_ptm_table(mycursor)
     # create_alignment_table(mycursor)

diff --git a/webApp/routes.py b/webApp/routes.py
@@ -194,7 +194,7 @@ def makeText(acc, gene, mutation, hmmPos, mycursor):
 			row = []
 			row.append(ref_gene)
 			# row.append(ref_acc)
-			row.append('<a href=\"https://www.uniprot.org/uniprot/'+acc+'\" target=\"_blank\">'+acc+'<i class="bi bi-box-arrow-in-up-right"></i></a>')
+			row.append('<a href=\"https://www.uniprot.org/uniprot/'+ref_acc+'\" target=\"_blank\">'+ref_acc+'<i class="bi bi-box-arrow-in-up-right"></i></a>')
 			row.append(ref_mutation[0])
 			row.append(ref_mutation[1:-1])
 			row.append(ref_mutation[-1])
@@ -597,7 +597,7 @@ def get_SummaryTable(**kwargs):
 				# 	text += '<br><b>More information:</b><br>' + row['text']
 				# break
 
-		dic = {'data': data, 'acc': acc}
+		dic = {'data': data, 'acc': acc, 'gene': gene}
 		return jsonify(dic)
 
 	@app.route('/AJAXAlignment', methods=['GET', 'POST'])

diff --git a/webApp/static/js/showSummary.js b/webApp/static/js/showSummary.js
@@ -33,7 +33,7 @@ function defineSummaryDataTable (tableID, uniqID, kinase, mutation, results)
 							buttons: [
 								'copy', 'csv', 'excel', 'pdf', 'print', 'colvis',
 								{
-									text: "Show "+kinase+" instances only",
+									text: "Show "+response['gene']+" instances only",
 									action: function(e, dt, node, config){
 										dt.column(1).search(response['acc']).draw();
 									}