python筛选一样的_python如何筛选去除不想要的序列

我在做数千条序列系统发育时，可能有很多seq虽然名字不同但是序列一样，或者做某些分析时候需要做到没有简并碱基(datamonkey选择压力)，那么需要筛选。

以下为我写的python代码：

​#!/usr/bin/env python

fasta_file=open('pickcat.fas','r')

out_file = open('delambigous.derepeat.pickcat.fas','w')

seq=''

header = ''

UniqueSeq=[]

nucleotide={'A','G','T','C','a','t','c','g'}

#UniqueHeader=[]

for line in fasta_file:

line = line.strip()

if line[0] ==

'>' and seq =='':

# process the first line of the input file

header = line

elif line [0] !=

'>' and nucleotide|set(line) == nucleotide:

#del set(line) not in

ATGCagtc

# join the lines with sequence

seq = line

elif line [0] !=

'>' and nucleotide|set(line) != nucleotide:

header,seq= '',''

elif line[0] ==

'>' and seq != '':

# in subsequent lines starting with

'>',

# write the previous header and sequence

# to the output file. Then re-initialize

# the header and seq variables for the next

record

if seq not in UniqueSeq:   #

and header not in UniqueHeader:

UniqueSeq.append(seq) # and

UniqueHeader.append(header)

out_file.write(header+'\n'

+ seq+'\n')

seq,header= '',line

#'header = line' this BUG find me how

hard!!!!

fasta_file.close()

out_file.close()

这个脚本同时去除了简并碱基和序列名一致或者序列信息一致的

用的方法

去除一致序列

1.列表.append建立seq信息库；

2.查询读入的seq在不在信息库里面，不在就说明是新seq，立马append​；如果在信息库，说明有重复，则不输出序列​

去除简并碱基

​把set(seq)和{'A','G','T','C','a','t','c','g'}并集，看结果是否=={'A','G','T','C','a','t','c','g'}，从而判断是否有简并碱基，有则该seq和header不输出