How to modify fasta file headers

Question

[Paula]

Hi All!

I need to change modifty my fasta file headers in the follow way

Example

Input:

> Proteobacteria;_1 # 52 # 312 # 1 # ID=1_1;partial=01;start
> Firmicutes;_1 # 52 # 312 # 1 # ID=1_1;partial=01;start
> Planctomycetes;_1 # 52 # 312 # 1 # ID=1_1;partial=01;start

Output:

>Seq1
>Seq2
>Seq3

Thanks a lot!

[cpad0112]

Try one of these two:

$ awk '/^>/ {print ">Seq_"++n} !/^>/' input.fa
$ awk '/^>/ {sub(".*", ">Seq_"++n)}1' input.fa

Answer 1

[rpolicastro]

A seqkit answer.

Example 6 for seqkit replace is almost identical to your question with slight modification.

seqkit replace -p .+ -r "Seq{nr}"

[Paula]

Hi! One question, where should I put the input file? (sorry, I am new to this)

Thanks!

[rpolicastro]

You put it at the end.

seqkit replace -p .+ -r "Seq{nr}" old_file.fasta > new_file.fasta

[Paula]

Thanks broski!

Answer 2

[Pierre Lindenbaum]

awk '/^>/ {printf(">Seq%d\n",++N);next;} {print}' in.fa