#!/usr/bin/python"""USAGE: python *.py align_SNP_site out_file"""import sys#import timefrom collections import Counter#t0=time.clock()info=open(sys.argv[1])fast=sys.argv[2]d_c = {}d1={}d2={}for line in info:    cols=line.strip().split("/t")    if cols[0] == "SNP pattern":        continue    else:        d1.setdefault(cols[4],[]).append(cols[1])        d2.setdefault(cols[7],[]).append(cols[1])    #d1.setdefault(cols[0],[]).append(cols[5])    #d2[cols[0]] = "/t".join(cols[0:3])info.close()print len(d1)print len(d2)my_list=[]ref_fa = open("some_example.fasta", 'r')for i in ref_fa.readlines():    if i.startswith(">"):        my_list.append(i.rstrip())ref_fa.close()print len(my_list)#sys.exit()result = open(fast,'w')for k,v in d1.iteritems():    cnt1 = Counter(v)    #print cnt1    result.write("%s/t" % k)    for i in sorted(cnt1.items(), key = lambda x: x[1], reverse=True):        result.write("%s/t%d/t"%(i[0],i[1]))    result.write("/n")for k,v in d2.iteritems():    cnt2 = Counter(v)    #print cnt2    result.write("%s/t" % k)    for i in sorted(cnt2.items(), key = lambda x: x[1], reverse=False):        result.write("%s/t%d/t"%( i[0],i[1]))    result.write("/n")#t1=time.clock()#print (t1-t0)