Question

我有一个FASTA文件（testfile.fa），其中包含标题行（在开头包含＆gt;）和带有字符的行，表示某些类型的核苷酸（A，C，G，T，a，g，c， t，N）。

>chr1
cccccccccttttttttaaaa
AAAACCCCTTCCCCCCCCGGG
GGGGGGGGGGGGGGGGGGGGG
TTTTTTTTTTTTTTTTTTTTT
>chr1_alt
TCTCTCTCTCTCTCTCTCTCT
gggtttccccccccccccccc
CGCGCGCGCGCGCGCGCGCGC
CCCCCAAAAAAAAAAAAAAAA
>chr2
CCCCCCCCCCCCCCCCCCCCC
TTTTTTTTTTTTATTTTTTTT
>chr3
AAAAAAAAAAAAAAAAAAAAA
GGGGGGGGGGGGGGGGGGGGG
TTTTTTTTTTTTTTTTTTTTT

我需要逐行读取此文件，并在除标题之外的每个序列中将小字符（a，c，t，g）更改为N，其中包含＆gt;。所以我使用以下代码：

#!/bin/bash 
while read line
do
    if [[ $line =~ ">" ]]
    then
        echo $line
    else
        tr 'c' 'N'
        echo $line
    fi
done < testfile.fa

但结果令人困惑：

>chr1
# the first line was missed
AAAACCCCTTCCCCCCCCGGG
GGGGGGGGGGGGGGGGGGGGG
TTTTTTTTTTTTTTTTTTTTT
>Nhr1_alt #the character was changed but the line contains >
TCTCTCTCTCTCTCTCTCTCT
gggtttNNNNNNNNNNNNNNN
CGCGCGCGCGCGCGCGCGCGC
CCCCCAAAAAAAAAAAAAAAA
>Nhr2 #the character was changed but the line contains >
CCCCCCCCCCCCCCCCCCCCC
TTTTTTTTTTTTATTTTTTTT
>Nhr3 #the character was changed but the line contains >
AAAAAAAAAAAAAAAAAAAAA
GGGGGGGGGGGGGGGGGGGGG
TTTTTTTTTTTTTTTTTTTTTcccccccccttttttttaaaa #the first line from the first sequence comes here

这些问题的可能原因是什么，我该如何解决？提前谢谢！

Answer 1

使用awk：

$ awk '/^[^>]/{gsub(/[actg]/,"N")}1' file
>chr1
NNNNNNNNNNNNNNNNNNNNN
AAAACCCCTTCCCCCCCCGGG
GGGGGGGGGGGGGGGGGGGGG
TTTTTTTTTTTTTTTTTTTTT
>chr1_alt
TCTCTCTCTCTCTCTCTCTCT
NNNNNNNNNNNNNNNNNNNNN
CGCGCGCGCGCGCGCGCGCGC
CCCCCAAAAAAAAAAAAAAAA
>chr2
CCCCCCCCCCCCCCCCCCCCC
TTTTTTTTTTTTATTTTTTTT
>chr3
AAAAAAAAAAAAAAAAAAAAA
GGGGGGGGGGGGGGGGGGGGG
TTTTTTTTTTTTTTTTTTTTT

说明：

/^[^>]/ {               # if the record starts with anything but >
    gsub(/[actg]/,"N")  # replace all actg with N
}1                      # output

Answer 2

您以错误的方式使用tr。

这是我的剧本：

#!/bin/sh

while read line
do
    if [[ $line =~ ">" ]]
    then
        echo $line
    else
        echo $line | tr 'c' 'N'
    fi
done < t.file

Answer 3

要使用awk语句更改所有小写变量，我们可以使用：

awk '{ if (substr($0,1,1) != ">") { stat="";for ( i=1;i<=length($0);i++ ) { if ( substr($0,i,1) ~ /[[:lower:]]/ ) { stat=stat"N" } else stat=stat substr($0,i,1) } print stat } else { print $0 } }' testfile.fa

我们使用awk的substr函数，只需用＆gt;打印任何行。作为第一个角色。使用其他行，我们构建一个变量stat，将所有小写字母更改为N，然后打印最终的stat结果。

Answer 4

sed是实现这一目标的简单方法：

sed -i '/^>/ !s/[actg]/N/g' testfile.fa

[]包含将更改为N的字符，/^>/ !部分忽略以＆gt;开头的行

-i将覆盖当前文件，如果没有它，您将获得标准输出的输出。

如何逐行读取文件，如果行包含特定值，则更改字符

4 个答案: