@sjcrh/proteinpaint-server 2.105.0 → 2.106.0

package/utils/gsea.py

@@ -1,129 +1,140 @@
-# cat ~/sjpp/test.txt | python gsea.py
+# Test syntax: cat ~/sjpp/test.txt | time python gsea.py
+# test.txt contains the json string autogenerated by the commented out nodejs code.
+import blitzgsea as blitz  
+import json 
+import time  
+import sys  
+import sqlite3  
+import os  
+import numpy as np  
+import pandas as pd  
 
-import blitzgsea as blitz
-import json
-import time
-import sys
-import sqlite3
-import os
-import numpy as np
-import pandas as pd
-            
+# Helper function to extract gene symbols from a dictionary
 def extract_symbols(x):
-   return x['symbol']
-
-def extract_plot_data(signature, geneset, library, result, center=True):
-   signature = signature.copy()
-   signature.columns = ["i","v"]
-   signature = signature.sort_values("v", ascending=False).set_index("i")
-   signature = signature[~signature.index.duplicated(keep='first')]
-   if center:
-       signature.loc[:,"v"] -= np.mean(signature.loc[:,"v"])
-   signature_map = {}
-   for i,h in enumerate(signature.index):
-       signature_map[h] = i
-   
-   gs = set(library[geneset])
-   hits = [i for i,x in enumerate(signature.index) if x in gs]
-   
-   running_sum, es = blitz.enrichment_score(np.array(np.abs(signature.iloc[:,0])), signature_map, gs)
-   running_sum = list(running_sum)
-   nn = np.where(np.abs(running_sum)==np.max(np.abs(running_sum)))[0][0]
-   #print ("nn:",nn)
-   #print ("running_sum:",running_sum)
-   #print ("es:",es)
-   running_sum_str=[str(elem) for elem in running_sum]
-   print ('result: {"nn":'+str(nn)+',"running_sum":"'+",".join(running_sum_str)+'","es":'+str(es)+'}')
+    return x['symbol']  # Return the 'symbol' field from the dictionary
 
-
-# Main function   
+# Main function
 try:
-    # Try to read a single character from stdin without blocking
+    # Check if there is input from stdin
     if sys.stdin.read(1):
-        # Read from stdin
+        # Read each line from stdin
         for line in sys.stdin:
-            # Process each line
+            # Parse the JSON input
             json_object = json.loads(line)
-            cachedir=json_object['cachedir']
-            genes=json_object['genes']
-            fold_change=json_object['fold_change']
-            table_name=json_object['geneset_group']
-            filter_non_coding_genes=json_object['filter_non_coding_genes']
-            df = {'Genes': genes, 'fold_change': fold_change}
-            signature=pd.DataFrame(df)
-            db=json_object['db']
-            # 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)
-            if filter_non_coding_genes == True:
-                 # SQL query to code all the protein coding genes
-                 coding_genes_query = f"select * from codingGenes"
-                 genedb = json_object['genedb']
-                 gene_conn = sqlite3.connect(genedb)
-                 gene_cursor = gene_conn.cursor()
-                 gene_cursor.execute(coding_genes_query)
-                 coding_genes_list=gene_cursor.fetchall()
-                 coding_genes_list=list(map(lambda x: x[0],coding_genes_list))
-                 signature=signature[signature['Genes'].isin(coding_genes_list)]
-                 
-            # 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))
+            cachedir = json_object['cachedir']  # Get the cache directory from the JSON object
+            genes = json_object['genes']  # Get the genes from the JSON object
+            fold_change = json_object['fold_change']  # Get the fold change values from the JSON object
+            table_name = json_object['geneset_group']  # Get the gene set group from the JSON object
+            filter_non_coding_genes = json_object['filter_non_coding_genes']  # Get the filter_non_coding_genes flag from the JSON object
+            db = json_object['db']  # Get the database path from the JSON object
+            # Create a DataFrame for the signature
+            df = {'Genes': genes, 'fold_change': fold_change}  # Create a dictionary with genes and fold change
+            signature = pd.DataFrame(df)  # Convert the dictionary to a DataFrame
             
-            #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")
-            try: # Extract ES data to be plotted on client side
-               geneset_name=json_object['geneset_name'] # Checks if geneset_name is present, if yes it indicates the server request is for generating the image. It retrieves the result.pkl file and generates the image without having to recompute gsea again.
-               pickle_file=json_object['pickle_file']
-               result = pd.read_pickle(os.path.join(cachedir,pickle_file))
-               fig = blitz.plot.running_sum(signature, geneset_name, msigdb_library, result=result.T, compact=True)
-               random_num = np.random.rand()
-               png_filename = "gsea_plot_" + str(random_num) + ".png"
-               fig.savefig(os.path.join(cachedir,png_filename), bbox_inches='tight')
-               #extract_plot_data(signature, geneset_name, msigdb_library, result) # This returns raw data to client side, not currently used
-               print ('image: {"image_file":"' + png_filename + '"}')
-            except KeyError: #Initial GSEA calculation, result saved to a result.pkl pickle file               
-               # run enrichment analysis
-               start_gsea_time = time.time()
-               if __name__ == "__main__":
-                  result = blitz.gsea(signature, msigdb_library).T
-                  random_num = np.random.rand()
-                  pickle_filename="gsea_result_"+ str(random_num) +".pkl"
-                  result.to_pickle(os.path.join(cachedir,pickle_filename))
-                  gsea_str='{"data":' + result.to_json() + '}'
-                  pickle_str='{"pickle_file":"' + pickle_filename + '"}'
-                  #print ("pickle_file:",pickle_str)
-                  gsea_dict = json.loads(gsea_str)
-                  pickle_dict = json.loads(pickle_str)
-                  result_dict = {**gsea_dict, **pickle_dict}
-                  print ("result:",json.dumps(result_dict))
-               stop_gsea_time = time.time()   
-               gsea_time = stop_gsea_time - start_gsea_time
-               print (f"GSEA time: {gsea_time} seconds")
+            # Connect to the SQLite database
+            conn = sqlite3.connect(db)  # Connect to the SQLite database
+            cursor = conn.cursor()  # Create a cursor object
+
+            msigdb_library = {}  # Initialize an empty dictionary for the gene set library
+            if table_name == "REACTOME--blitzgsea": # Parse from blitzgsea reactome library
+              msigdb_library = blitz.enrichr.get_library("Reactome_2022")
+            elif table_name == "KEGG--blitzgsea": # Parse from blitzgsea KEGG library
+              msigdb_library = blitz.enrichr.get_library("KEGG_2021_Human")
+            elif table_name == "WikiPathways--blitzgsea": # Parse from blitzgsea WikiPathways library
+              msigdb_library = blitz.enrichr.get_library("WikiPathways_2019_Human")              
+            else: # Use geneset groups from msigdb    
+              # Query to get gene set IDs
+              query = f"SELECT id FROM terms WHERE parent_id='{table_name}'"  # SQL query to get gene set IDs
+              cursor.execute(query)  # Execute the query
+              
+              # Fetch all gene set IDs
+              rows = cursor.fetchall()  # Fetch all rows from the executed query
+              
+              start_loop_time = time.time()  # Record the start time of the loop
+              
+              # Iterate over gene set IDs and fetch corresponding genes
+              for row in rows:
+                  query2 = f"SELECT genes FROM term2genes WHERE id='{row[0]}'"  # SQL query to get genes for a gene set ID
+                  cursor.execute(query2)  # Execute the query
+                  rows2 = cursor.fetchall()  # Fetch all rows from the executed query
+                  row3 = json.loads(rows2[0][0])  # Parse the JSON data
+                  msigdb_library[row[0]] = list(set(map(extract_symbols, row3)))  # Extract only unique gene symbols and add them to the library. "set" command selects only unique genes 
+              #print ("msigdb_library:",msigdb_library) 
+                  
+              # Close the cursor and connection to the database
+              cursor.close()  # Close the cursor
+              conn.close()  # Close the connection
+              
+              stop_loop_time = time.time()  # Record the stop time of the loop
+              execution_time = stop_loop_time - start_loop_time  # Calculate the execution time
+              print(f"Execution time: {execution_time} seconds")  # Print the execution time
+
+            # Filter out non-coding genes if specified
+            if filter_non_coding_genes:
+                coding_genes_query = "SELECT * FROM codingGenes"  # SQL query to get coding genes
+                genedb = json_object['genedb']  # Get the gene database path from the JSON object
+                gene_conn = sqlite3.connect(genedb)  # Connect to the gene database
+                gene_cursor = gene_conn.cursor()  # Create a cursor object for the gene database
+                gene_cursor.execute(coding_genes_query)  # Execute the query to get coding genes
+                coding_genes_list = gene_cursor.fetchall()  # Fetch all coding genes
+                coding_genes_list = list(map(lambda x: x[0], coding_genes_list))  # Extract the gene symbols
+                signature = signature[signature['Genes'].isin(coding_genes_list)]  # Filter the signature to include only coding genes
             
+            try:
+                # Check if geneset_name and pickle_file are present for generating the plot
+                geneset_name = json_object['geneset_name']  # Get the gene set name from the JSON object
+                pickle_file = json_object['pickle_file']  # Get the pickle file name from the JSON object
+                result = pd.read_pickle(os.path.join(cachedir, pickle_file))  # Load the result from the pickle file
+                fig = blitz.plot.running_sum(signature, geneset_name, msigdb_library, result=result.T, compact=True)  # Generate the running sum plot
+                random_num = np.random.rand()  # Generate a random number for unique png filename
+                png_filename = f"gsea_plot_{random_num}.png"  # Create a filename for the plot
+                fig.savefig(os.path.join(cachedir, png_filename), bbox_inches='tight')  # Save the plot as a PNG file
+                print(f'image: {{"image_file": "{png_filename}"}}')  # Print the image file path in JSON format
+            except KeyError:
+                # Initial GSEA calculation and save the result to a pickle file
+                start_gsea_time = time.time()  # Record the start time of GSEA
+                if __name__ == "__main__":
+                    num_permutations = json_object['num_permutations'] # Number of permutations for GSEA analysis
+                    result = blitz.gsea(signature, msigdb_library, permutations=num_permutations).T  # Perform GSEA and transpose the result
+                    random_num = np.random.rand()  # Generate a random number for unique pickle filename
+                    pickle_filename = f"gsea_result_{random_num}.pkl"  # Create a filename for the pickle file
+                    result.to_pickle(os.path.join(cachedir, pickle_filename))  # Save the result to the pickle file
+                    gsea_str = f'{{"data": {result.to_json()}}}'  # Convert the result to JSON format
+                    pickle_str = f'{{"pickle_file": "{pickle_filename}"}}'  # Create a JSON string for the pickle file
+                    gsea_dict = json.loads(gsea_str)  # Parse the JSON string
+                    pickle_dict = json.loads(pickle_str)  # Parse the JSON string
+                    result_dict = {**gsea_dict, **pickle_dict}  # Merge the dictionaries
+                    print(f"result: {json.dumps(result_dict)}")  # Print the result in JSON format
+                stop_gsea_time = time.time()  # Record the stop time of GSEA
+                gsea_time = stop_gsea_time - start_gsea_time  # Calculate the GSEA execution time
+                print(f"GSEA time: {gsea_time} seconds")  # Print the GSEA execution time
     else:
-       pass 
+        pass  # Do nothing if there is no input from stdin
 except (EOFError, IOError):
-    pass
+    pass  # Handle EOFError and IOError exceptions gracefully
+
+# Function to extract plot data for GSEA visualization (NOT currently being used, but will be used for generating client side gsea plots)
+def extract_plot_data(signature, geneset, library, result, center=True):
+     print("signature", signature)
+     print("result", result)
+     print("geneset", geneset)
+     print("library", library)
+     signature = signature.copy()  # Create a copy of the signature DataFrame
+     signature.columns = ["i", "v"]  # Rename columns to 'i' and 'v'
+     signature = signature.sort_values("v", ascending=False).set_index("i")  # Sort by 'v' in descending order and set 'i' as index
+     signature = signature[~signature.index.duplicated(keep='first')]  # Remove duplicate indices, keeping the first occurrence
+   
+     if center:
+         signature.loc[:, "v"] -= np.mean(signature.loc[:, "v"])  # Center the signature values by subtracting the mean
+   
+     signature_map = {h: i for i, h in enumerate(signature.index)}  # Create a mapping of signature indices
+   
+     gs = set(library[geneset])  # Get the gene set from the library
+     hits = [i for i, x in enumerate(signature.index) if x in gs]  # Find the indices of hits in the signature
+   
+     running_sum, es = blitz.enrichment_score(np.array(np.abs(signature.iloc[:, 0])), signature_map, gs)  # Compute running sum and enrichment score
+     running_sum = list(running_sum)  # Convert running sum to a list
+     nn = np.where(np.abs(running_sum) == np.max(np.abs(running_sum)))[0][0]  # Find the index of the maximum absolute running sum
+   
+     running_sum_str = [str(elem) for elem in running_sum]  # Convert running sum elements to strings
+     print(f'result: {{"nn": {nn}, "running_sum": "{",".join(running_sum_str)}", "es": {es}}}')  # Print the result in JSON format