Trim fasta sequence names

Dear all,

I have bunch of fasta files with following sequence names format:

>gi|113476179|ref|YP_722240.1| hypothetical protein Tery_2568 [Trichodesmium erythraeum IMS101]

Do you have any script, which would help me to change it to something like this:

>Trichodesmium erythraeum IMS101

Thank you in advance!

Petr

fasta

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updated 4.0 years ago by Ram

• written 10.8 years ago by dvorikus •

1 answer

cat input.txt | sed 's/.*\[/>/' | sed 's/\]//'

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updated 4.0 years ago by Ram

• written 10.8 years ago by Biomonika (Noolean)

It did exactly, what I needed. Thank you Noolean!

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written 10.7 years ago by dvorikus •

Glad to help! Please also upvote my answer by clicking on the thumbs up green icon:)

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written 10.7 years ago by Biomonika (Noolean)

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