diff cmpb2016/pub_clono_CDR3.py @ 0:8be019b173e6 draft

Uploaded included tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cmpb2016/pub_clono_CDR3.py	Sun Mar 18 05:54:20 2018 -0400
@@ -0,0 +1,75 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Dec 21 18:26:01 2015
+
+@author: chmaramis
+"""
+
+from __future__ import division
+import numpy as np
+from pandas import *
+from numpy import nan as NA
+import sys
+import time
+
+
+
+def publicCDR3Func(inputs,thres):
+    
+    cdr3=DataFrame()
+
+    for x in range(0,len(inputs),2):
+            cl = DataFrame()
+            cl = read_csv(inputs[x] , sep = '\t' , index_col = 0)
+            #tp = read_csv(inp_name, iterator=True, chunksize=5000,sep='\t', index_col=0 )
+            #cl = concat([chunk for chunk in tp]) 
+            
+            if (thres != 'null'):
+                cl = cl[cl['Reads'] > int(thres)]
+            
+            x1 = inputs[x+1].split('_')
+            
+            del cl['Reads']
+            cl.columns = [cl.columns[0], x1[0]+' '+cl.columns[1], x1[0]+' Relative '+cl.columns[2]]
+            
+            if cdr3.empty:
+                cdr3 = cl
+            else:
+                cdr3 = cdr3.merge(cl, how='outer', on='AA JUNCTION')
+    
+    
+    col = cdr3.columns
+    freqs = col.map(lambda x: 'Frequency' in x)
+    reads = col.map(lambda x: 'Reads/Total' in x)
+    
+    cdr3[col[freqs]] = cdr3[col[freqs]].fillna(0)
+    cdr3[col[reads]] = cdr3[col[reads]].fillna('0/*')
+    
+    cdr3['Num of Patients']= cdr3[col[freqs]].apply(lambda x: np.sum(x != 0), axis=1)
+
+    cdr3 = cdr3[cdr3['Num of Patients'] > 1]
+
+    cdr3.index = range(1,len(cdr3)+1)
+    
+    return cdr3    
+
+
+if __name__ == '__main__':   
+
+    start=time.time()    
+    
+    # Parse input arguments
+    threshold = sys.argv[2]
+    arg = sys.argv[3:]
+    output = sys.argv[1]
+        
+    # Execute basic function
+    mer = publicCDR3Func(arg,threshold)
+    
+    # Save output to CSV files
+    if not mer.empty:
+        mer.to_csv(output , sep = '\t') 
+
+    # Print execution time
+    stop=time.time()
+    print('Runtime:' + str(stop-start))