help to edit fasta header

Dear All,

I would like to edit the header of a multifasta file, but I am not so familiar with scripting.

Basically, I want to remove information within parenthesis (including the symbols) and remove bracket symbols, but miantaining the information within. for instance,

>gi|745831934|gb|AJD39620.1| protein A (plasmid) [Homo sapiens]
>gi|745831934|gb|AJD39620.1| protein A Homo sapiens

Thanks in advance

sequence alignment

• 4,476 views • link

updated 4.0 years ago by Ram

• written 10.5 years ago by mario.t.murakami •

1 answer

perl -pe 's/\(.*\)//' file.faa | sed 's/\[//' | sed 's/\]//'

or (Updated)

perl -pe 's/\(.*\)//' file.faa | perl -pe 's/\[//' | perl -pe 's/\]//'

• 0 views • link

updated 7.2 years ago by Ram

• written 10.5 years ago by venu

Dear Venu,

Thanks for your help. When I run your suggested command line I got the following error:

sed: -e expression #1, char 1: unknown command: ` ' '

Please, tell me how to write into an output file and not only printing on the screen. thanks again.

• 0 views • link

updated 7.2 years ago by Ram

• written 10.5 years ago by mario.t.murakami •

You can redirect the output to a new file like this:

$ perl -pe 's/\(.*\)//' file.faa | sed 's/\[//' | sed 's/\]//' > new_file_name

• 0 views • link

updated 7.2 years ago by Ram

• written 10.5 years ago by GenoMax

Yes, I did it. but it is just writing the original file. PS: I tested it without the sed commands.

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updated 7.2 years ago by Ram

• written 10.5 years ago by mario.t.murakami •

Are you saying that you are still getting the sed error you mentioned above? Are you using the command exactly as provided by @venu (with single quote characters)?

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updated 7.2 years ago by Ram

• written 10.5 years ago by GenoMax

I mean that the changes that should be done by the command are not written in the output file.

by the way the command line updated by @venu is not working the second and third part. it is now only printing like that:

original: >gi|745831934|gb|AJD39620.1| protein A (plasmid) [Homo sapiens]
printed: >gi|745831934|gb|AJD39620.1| protein A [Homo sapiens]

perhaps is it related with fact that I am using strawberry perl in windows os?

thanks

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updated 6.6 years ago by Ram

• written 10.5 years ago by mario.t.murakami •

Obviously there is perl on unix and the perl you are using on windows, which does not appear to work the way we expect it to on unix.

Is this file large to not be able to do this using an editor in windows?

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updated 7.2 years ago by Ram

• written 10.5 years ago by GenoMax

yes, there are 400 sequences. I will run the script on linux and it will probably work fine.

thanks

• 0 views • link

written 10.5 years ago by mario.t.murakami •

It's perfectly working fine. I don't know why you are getting error. I am updating answer. Direct the output to new file as @genomax said.

• 0 views • link

updated 6.6 years ago by Ram

• written 10.5 years ago by venu

thanks both. On linux, it worked fine.

• 0 views • link

updated 6.6 years ago by Ram

• written 10.5 years ago by mario.t.murakami •