perl python文本处理_Python和Perl处理fasta文件对比_2018-09-11

从fasta中抽取需要的序列：

Python方法一：(这种方式最慢)

由于平时工作比较忙，工作中遇到的问题都没有及时记录，现在有空时间了所以整理一下一些常见的问题及技巧供大家参考：

!/usr/bin/python

import sys

def Fasta(inputfile) :

f = open(inputfile,"r")

fastadic = {}

while True :

line = f.readline().rstrip()

if len(line) == 0 :

break

else :

pass

if line.startswith(">") :

name = line.split()[0]

fastadic[name] = ""

else :

fastadic[name]+=line

f.close()

return fastadic

def usage():

print ("1,fasta\n2,list")

if len(sys.argv) != 3 :

usage()

sys.exit()

print (sys.argv[0])

fastafile = sys.argv[1]

listfile = sys.argv[2]

dic = Fasta(fastafile)

ff=open(listfile,"r")

while 1:

line1 = ff.readline().rstrip()

if len(line1) == 0 :

break

else :

pass

array = line1.split("\t")

if ">"+array[0] in dic.keys() :

print (">"+array[0]+"\n"+dic[">"+array[0]])

else :

print ("Error:"+line1)

ff.close()

Python方法二：(次慢)

!/usr/bin/python

import sys

def Fasta(inputfile) :

f = open(inputfile,"r")

fastadic = {}

while True :

line = f.readline().rstrip()

if len(line) == 0 :

break

else :

pass

if line.startswith(">") :

name = line.split()[0]

fastadic[name] = []

else :

fastadic[name].append(line)

f.close()

return fastadic

def usage():

print ("1,fasta\n2,list")

if len(sys.argv) != 3 :

usage()

sys.exit()

print (sys.argv[0])

fastafile = sys.argv[1]

listfile = sys.argv[2]

dic = Fasta(fastafile)

ff=open(listfile,"r")

while 1:

line1 = ff.readline().rstrip()

if len(line1) == 0 :

break

else :

pass

array = line1.split("\t")

if ">"+array[0] in dic.keys() :

print (">"+array[0]+"\n"+"".join(dic[">"+array[0]]))

else :

print ("Error:"+line1)

ff.close()

Perl 方法三(最快)

!/usr/bin/perl -w

die "perl

ARGV[0] ;

while () {

chomp;

if (/^>/) {

@name = split/\s+/,

fasta{

fasta{

_ ；

}

}

close I;

open T,

_ ;

if (exists

tax[0]}) {

print ">".

fasta{">".$tax[0]}, "\n" ;

}

}

close T;