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This article mainly introduces Python's method of using defaultdict to read each column of a file, involving Python's file-related reading and traversal operation skills. Friends in need can refer to it
The examples in this article describe the use of Python defaultdict method to read each column of the file. Share it with everyone for your reference, the details are as follows:
#!/usr/bin/python """USAGE: python *.py align_SNP_site out_file""" import sys #import time from 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)
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