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Modify fasta file header

I am a newbi for linux stuff... I would like to modify the header of fasta file. My header is like: >100123_00010T gene=100123_00010 And, I would like to have headers like "100123_00010"

Would you give me some advise to get that result?

fastfile modification
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updated by rpolicastro rpolicastro • written by hellokwmin • hellokwmin

This is a frequently asked question on biostars with many answers.

$ cut -d ' ' -f1 your_file.fa
>100123_00010T
AAA

will most likely suffice.

If you remove the leading > then the file will no longer be in fasta format.

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written by GenoMax GenoMax 
cat test.fa| awk '{if(/^>/){print $1}else {print $0}}'
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written by size_t • size_t

For a fasta you could just do awk '{print $1}' test.fa

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written by rpolicastro rpolicastro

Here are some other options. It's good to try a search first when you have questions.

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written by seidel seidel

1 answer

obligatory seqkit answer

seqkit replace -p ".+gene=(.+)" -r "\$1" input.fa -o output.fa
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written by rpolicastro rpolicastro

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