Mercurial > repos > chmaramis > irprofiler
view clonotype_computation.py @ 1:acaa8e8a0b88 draft default tip
Uploaded test-data & added tool help
author | chmaramis |
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date | Mon, 30 Apr 2018 04:47:52 -0400 |
parents | 0e37e5b73273 |
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# -*- coding: utf-8 -*- """ Created on Sat Mar 24 14:00:24 2018 @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) clono_def = {'CDR3': ['AA JUNCTION'], 'VCDR3': ['V-GENE','AA JUNCTION'], 'JCDR3': ['J-GENE','AA JUNCTION'], 'VJCDR3': ['V-GENE','J-GENE','AA JUNCTION'], 'VDJCDR3': ['V-GENE','D-GENE','J-GENE','AA JUNCTION']} def clonotypeComputation(inp_name, clono, out1, t10n, fname): clono_comps = clono_def[clono] 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(clono_comps) x=grouped.size() x1=DataFrame(list(x.index), columns=clono_comps) 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[clono_comps + ['Frequency %']].head(10) top10.to_csv(t10n , sep = '\t') summary = [[clono]] summary.append([', '.join([top10[c].values[0] for c in clono_comps])]) 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 = ['Clonotype Definition', 'Dominant Clonotype', '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] clono = sys.argv[2] out1 = sys.argv[3] t10n = sys.argv[4] sname = sys.argv[5] fname = sys.argv[6] # Execute basic function frsum = clonotypeComputation(inp_name, clono, 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))