Replace fasta Header witha a matching text
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9 months ago
Optimist ▴ 170

My fasta header looks like this

>name1
ATGCATGCAT

My output must look like this

>alfaAB

--kv file looks like this

name1        alfaAB

What command can be used to achieve this??

Thank You

awk seqkit grep • 603 views
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Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

What is --kv? Is that a seqkit option? If you are using seqkit then please post the command you are using by editing the original post.

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I want to know what command can be used to achieve the purpose.

It can be seqkit or anything else

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9 months ago
GenoMax 110k
$ more test.fa
>name1
ATGCATGCAT
>name2
AGCTAGC

$ more names
name1   alfaAB
name2   alfaCD

$ seqkit replace -p "(.+)" -r '{kv}' -k names test.fa
[INFO] read key-value file: names
[INFO] 2 pairs of key-value loaded
>alfaAB
ATGCATGCAT
>alfaCD
AGCTAGC
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This worked

Thanks a ton

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