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Author: xiaoyao00

LDlink/LDcommon.py

@@ -276,9 +276,10 @@ def getRefGene(db, filename, chromosome, begin, end, genome_build, collapseTrans
                 "txEnd": {"$gte": int(end)}
             }
         ]
-    })
+    })#.sort([("cdsEnd",1),("txStart",1)])
     if collapseTranscript:
         query_results_sanitized = json.loads(json_util.dumps(query_results)) 
+        #print("$$$$$$",query_results_sanitized)
         group_by_gene_name = {}
         for gene in query_results_sanitized:
             # new gene name
@@ -288,13 +289,17 @@ def getRefGene(db, filename, chromosome, begin, end, genome_build, collapseTrans
             # same gene name as another's
             else:
                 group_by_gene_name[gene['name2']].append(gene)
-        # print(json.dumps(group_by_gene_name, indent=4, sort_keys=True))
+        print(json.dumps(group_by_gene_name, indent=4, sort_keys=False))
         query_results_sanitized = []
         for gene_name_key in group_by_gene_name.keys():
+            #print("#",gene_name_key)
             query_results_sanitized.append(processCollapsedTranscript(group_by_gene_name[gene_name_key]))
         # print(json.dumps(query_results_sanitized, indent=4, sort_keys=True))
     else:
         query_results_sanitized = json.loads(json_util.dumps(query_results)) 
+    #temp = query_results_sanitized.pop(0)
+    #query_results_sanitized.append(temp)
+    print(query_results_sanitized)
     with open(filename, "w") as f:
         for x in query_results_sanitized:
             f.write(json.dumps(x) + '\n')

LDlink/LDproxy.py

@@ -50,7 +50,7 @@ def calculate_proxy(snp, pop, request, web, genome_build, r2_d="r2", window=5000
     # Create JSON output
     out_json = open(tmp_dir + 'proxy' + request + ".json", "w")
     output = {}
-    print("######",request)
+
     validsnp(None,genome_build,None)
 
     if window < 0 or window > 1000000:
@@ -112,6 +112,7 @@ def calculate_proxy(snp, pop, request, web, genome_build, r2_d="r2", window=5000
     if coord1 < 0:
         coord1 = 0
     coord2 = int(snp_coord[genome_build_vars[genome_build]['position']]) + window
+    #print("#########",coord1,coord2)
     print("")
 
     # Calculate proxy LD statistics in parallel
@@ -697,7 +698,6 @@ def calculate_proxy(snp, pop, request, web, genome_build, r2_d="r2", window=5000
         else:
             genes_c_file = tmp_dir + "genes_c_" + request + ".json"
             genes_c_json = getRefGene(db, genes_c_file, snp_coord['chromosome'], int(coord1), int(coord2), genome_build, True)
-
             genes_c_plot_start=[]
             genes_c_plot_end=[]
             genes_c_plot_y=[]
@@ -764,7 +764,7 @@ def calculate_proxy(snp, pop, request, web, genome_build, r2_d="r2", window=5000
 
             data_gene_c_plot = {'exons_c_plot_x': exons_c_plot_x, 'exons_c_plot_yn': exons_c_plot_yn, 'exons_c_plot_w': exons_c_plot_w, 'exons_c_plot_h': exons_c_plot_h, 'exons_c_plot_name': exons_c_plot_name, 'exons_c_plot_id': exons_c_plot_id}
             source_gene_c_plot=ColumnDataSource(data_gene_c_plot)
-
+  
             max_genes_c = 40
             # if len(lines_c) < 3 or len(genes_c_raw) > max_genes_c:
             if len(lines_c) < 3: