diff comp_clono_CDR3.py @ 12:cdf95051bc55 draft default tip

Uploaded 2 tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/comp_clono_CDR3.py	Sun Mar 18 07:11:06 2018 -0400
@@ -0,0 +1,78 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Thu Jun 19 17:33:34 2014
+
+@author: chmaramis
+"""
+
+from __future__ import division
+import numpy as np
+from pandas import *
+import functools as ft
+import sys
+import time
+
+frm = lambda x,y: '{r}/{l}'.format(r=x,l=y) 
+    
+
+def cdr3Computation(inp_name, out1, t10n, fname):
+
+    frame = DataFrame()
+    tp = read_csv(inp_name, iterator=True, chunksize=5000,sep='\t', index_col=0 )
+    frame = concat([chunk for chunk in tp]) 
+
+    grouped = frame.groupby(['AA JUNCTION'])
+    x=grouped.size()
+    x1=DataFrame(x.index, columns=['AA JUNCTION'])
+    x1['Reads']=x.values
+    total = sum(x1['Reads'])
+    #x1['Reads/Total'] = ['{r}/{l}'.format(r=pr , l = total) for pr in x1['Reads']]
+    x1['Reads/Total'] = x1['Reads'].map(ft.partial(frm, y=total))
+    x1['Frequency %'] = (100*x1['Reads']/total).map('{:.4f}'.format)
+
+    final = x1.sort_values(by = ['Reads'] , ascending = False)
+    
+    final.index=range(1,len(final)+1)
+    final.to_csv(out1 , sep = '\t')
+    
+    numofclono = len(final)
+    clust = len(final[final['Reads'] > 1])
+    sing = len (final[final['Reads'] == 1])
+    top10 = final[['AA JUNCTION','Frequency %']].head(10)
+    top10.to_csv(t10n , sep = '\t')
+    
+    summary = [[str(top10['AA JUNCTION'].values[0])]]
+    summary.append([top10['Frequency %'].values[0]])
+    summary.append([numofclono])
+    summary.append([clust,'{:.4f}'.format(100*clust/numofclono)])
+    summary.append([sing,'{:.4f}'.format(100*sing/numofclono)])
+    
+    ind = ['Dominant Clonotype (CDR3)', 'Frequency', 'Number of Clonotypes' , 'Expanding Clonotypes','Singletons']
+    spl = fname.split('_')
+    col = [spl[0],'%']
+    
+    frsum = DataFrame(summary,index = ind, columns = col)
+    
+    return frsum
+
+if __name__ == '__main__':   
+
+    start=time.time()
+
+    # Parse input arguments    
+    inp_name = sys.argv[1]
+    out1 = sys.argv[2]
+    t10n = sys.argv[3]
+    sname = sys.argv[4]
+    fname = sys.argv[5]
+            
+    # Execute basic function
+    frsum = cdr3Computation(inp_name,out1,t10n,fname)
+    
+    # Save output to CSV files
+    if not frsum.empty: 
+        frsum.to_csv(sname, sep = '\t')
+        
+    # Print execution time
+    stop=time.time()
+    print('Runtime:' + str(stop-start))