linux 中 shell 实现从fasta中提取任意的scaffold数据

 

001、测试数据

[root@pc1 test2]# ls
a.fa
[root@pc1 test2]# cat a.fa    ## 测试数据
>chr1
ddtttggggg
eeeeee
>chr2
iiiiirrrr
sssssssss
>chr3
uuuuueeeee
qqqqqqqqq
>chr4
tttttttt
wwwwwww
>chr5
yyyyyyy
ggggggg

 

 

 

002、sed命令实现提取任意的scaffold数据：

提取scaffold1

[root@pc1 test2]# cat a.fa
>chr1
ddtttggggg
eeeeee
>chr2
iiiiirrrr
sssssssss
>chr3
uuuuueeeee
qqqqqqqqq
>chr4
tttttttt
wwwwwww
>chr5
yyyyyyy
ggggggg
[root@pc1 test2]# sed -n '/^>chr1/,/^>/p' a.fa | sed '1b; />/d'   ## 提取scaffold1
>chr1
ddtttggggg
eeeeee

 

 

003、提取scaffold3

[root@pc1 test2]# ls
a.fa
[root@pc1 test2]# cat a.fa       ## 测试数据
>chr1
ddtttggggg
eeeeee
>chr2
iiiiirrrr
sssssssss
>chr3
uuuuueeeee
qqqqqqqqq
>chr4
tttttttt
wwwwwww
>chr5
yyyyyyy
ggggggg
[root@pc1 test2]# sed -n '/^>chr3/,/^>/p' a.fa | sed '1b; />/d'   ## 提取scaffold3
>chr3
uuuuueeeee
qqqqqqqqq

 

 

004、提取scaffold5

[root@pc1 test2]# ls
a.fa
[root@pc1 test2]# cat a.fa            ## 测试数据
>chr1
ddtttggggg
eeeeee
>chr2
iiiiirrrr
sssssssss
>chr3
uuuuueeeee
qqqqqqqqq
>chr4
tttttttt
wwwwwww
>chr5
yyyyyyy
ggggggg
[root@pc1 test2]# sed -n '/^>chr5/,/^>/p' a.fa | sed '1b; /^>/d'    ## 提取scaffold5
>chr5
yyyyyyy
ggggggg