How to modify fasta file headers
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23 months ago
Paula ▴ 60

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!

fasta • 799 views
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0
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Try one of these two:

$ awk '/^>/ {print ">Seq_"++n} !/^>/' input.fa
$ awk '/^>/ {sub(".*", ">Seq_"++n)}1' input.fa
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2
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23 months ago

A seqkit answer.

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

seqkit replace -p .+ -r "Seq{nr}"
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0
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Hi! One question, where should I put the input file? (sorry, I am new to this)

Thanks!

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1
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You put it at the end.

seqkit replace -p .+ -r "Seq{nr}" old_file.fasta > new_file.fasta
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1
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Thanks broski!

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2
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23 months ago
awk '/^>/ {printf(">Seq%d\n",++N);next;} {print}' in.fa
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