How to edit fasta header with underscores
Hi everyone! I want to remove one part of my fasta headers, could somebody help me??? please
I have this:
>Capsicum_annuum_cvCM334_CA01g24260 PREDICTED_ transmembrane 9 superfamily member 4-like [Solanum tuberosum]
MIAWISFPAVPLNFFGKEVVFSFATAVDNPLHVDLATQNKTRPSCAKVKMKINLLGEFPKRINVGMRMKTREVKEKGVNISYDYVPKYCKTFKLQDYNEKECFILHPKLYPKD
and I just want this part
>CA01g24260
MIAWISFPAVPLNFFGKEVVFSFATAVDNPLHVDLATQNKTRPSCAKVKMKINLLGEFPKRINVGMRMKTREVKEKGVNISYDYVPKYCKTFKLQDYNEKECFILHPKLYPKD
or
>CA01g24260 PREDICTED_ transmembrane 9 superfamily member 4-like [Solanum tuberosum]
MIAWISFPAVPLNFFGKEVVFSFATAVDNPLHVDLATQNKTRPSCAKVKMKINLLGEFPKRINVGMRMKTREVKEKGVNISYDYVPKYCKTFKLQDYNEKECFILHPKLYPKD
In my same fasta file, I have other sequences which are not in the same format as the sequence above:
>Capsicum_annuum_glabriusculum_Capang01g001768
VNKMENLQFVVIGKFTUEWTDIEELRNIIPQQCNINGDCQIGVFRNKHIF
IRUTQESDFINIIISKGAFYLHCKDVLLFDANTLTLIYDPLFKETLETTK
TFAWISFPNLLPTYYVKECLFSLAATVGKPVQLDLATINRTRPSCARIKV
LVDLKADFSKSVRMDIENEESGKCRTIVKRIKFDHIPKYCHECNMQVHAK
NQCRNL
But in general, I just want the last part:
>Capang01g001768
VNKMENLQFVVIGKFTUEWTDIEELRNIIPQQCNINGDCQIGVFRNKHIF
IRUTQESDFINIIISKGAFYLHCKDVLLFDANTLTLIYDPLFKETLETTK
TFAWISFPNLLPTYYVKECLFSLAATVGKPVQLDLATINRTRPSCARIKV
LVDLKADFSKSVRMDIENEESGKCRTIVKRIKFDHIPKYCHECNMQVHAK
NQCRNL
Because the program that I am using add the name of the species to the ID.
1 answer
Try this:
$ awk -v FS=" " '/^>/ {n=split($1, id, "_"); $0=">"id[n]}1' input.fasta > ouput.fasta
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input:
output:
Dear cpad0112, Could you help me with the questions that I pointed out below. Thank you.
I appreciate your answers, your scripts worked well for some kinds of sequences but not for all. The problem is that the headers of my sequences are not uniform. I have thirteen kinds of sequences (from different species = different headers). I want to extract the headers to get the CDS from another fasta file to carry out selection analysis. Therefore, I need that the headers can match with the headers of my CDS fasta file. For some reason, a previous analysis adds the name of the species to the original sequences headers.
These are the thirteen kinds of different sequences that I have and I am pointing out the header that I need:
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Thank for providing the detailed examples. This is not a trivial task, because there is no clean pattern for the names you like to keep.
So you have a file with "original sequence headers"? How does they look like there?
Hi! I have a .fasta file with proteins from every species. They look like this:
However, the program that I used to detect orthologues can give me also all the proteins sequences that belong to each ortogroup or gene family. Therefore, I want to carry out some analysis using Hyphy program, but this program required CDS sequences to work. So I also have all the CDS for each species. I need to use the headers from all the sequences that belong to each gene family (from Orthofinder) in order to obtain the CDS.