@sjcrh/proteinpaint-server 2.63.6 → 2.65.0

package/src/serverconfig.js

@@ -55,6 +55,7 @@ if (!serverconfig.clustalo) serverconfig.clustalo = 'clustalo'
 if (!serverconfig.Rscript) serverconfig.Rscript = 'Rscript'
 if (!serverconfig.gfServer) serverconfig.gfServer = 'gfServer'
 if (!serverconfig.gfClient) serverconfig.gfClient = 'gfClient'
+if (!serverconfig.python) serverconfig.python = 'python3'
 // NOTE: will set other cmd paths that require binpath after it's filled-in below
 
 /******************

package/utils/gsea.py

@@ -0,0 +1,75 @@
+# 'cat ~/sjpp/test.txt | python gsea.py
+
+import blitzgsea as blitz
+import json
+import time
+import sys
+import sqlite3
+import pandas as pd
+
+            
+def extract_symbols(x):
+   return x['symbol'] 
+
+try:
+    # Try to read a single character from stdin without blocking
+    if sys.stdin.read(1):
+        # Read from stdin
+        for line in sys.stdin:
+            # Process each line
+            json_object = json.loads(line)
+            db=json_object['db']
+            table_name=json_object['gene_set_group']
+            genes=json_object['genes']
+            fold_change=json_object['fold_change']
+            df = {'Genes': genes, 'fold_change': fold_change}
+            
+            # Connect to the SQLite database
+            conn = sqlite3.connect(db)
+            
+            # Create a cursor object using the cursor() method
+            cursor = conn.cursor()
+            
+            # SQL query to select all data from the table
+            query = f"select id from terms where parent_id='" + table_name  + "'"
+            
+            # Execute the SQL query
+            cursor.execute(query)
+            
+            # Fetch all rows from the executed SQL query
+            rows = cursor.fetchall()
+            
+            
+            start_loop_time = time.time()
+            msigdb_library={} 
+            # Iterate over the rows and print them
+            for row in rows:
+                #print(row[0])
+                query2=f"select genes from term2genes where id='" + row[0]  + "'"
+                cursor.execute(query2)
+                rows2 = cursor.fetchall()
+                row3=json.loads(rows2[0][0])
+                msigdb_library[row[0]] = list(map(extract_symbols,row3))
+            
+            #print ("msigdb_library:",msigdb_library)
+            # Close the cursor and connection to the database
+            cursor.close()
+            conn.close()
+            stop_loop_time = time.time()
+            execution_time = stop_loop_time - start_loop_time
+            print(f"Execution time: {execution_time} seconds")
+            signature=pd.DataFrame(df)
+            
+            # run enrichment analysis
+            start_gsea_time = time.time()
+            if __name__ == "__main__":
+               result = blitz.gsea(signature, msigdb_library).T
+               print ("result:",result.to_json())
+            stop_gsea_time = time.time()   
+            gsea_time = stop_gsea_time - start_gsea_time
+            print (f"GSEA time: {gsea_time} seconds")
+            
+    else:
+       pass 
+except (EOFError, IOError):
+    pass