Extraction Of Header Of Sequences In Fasta File

Question

[Mohammad Reza Bakhtiarizadeh]

Hi all I have a fasta file that i want to extract just header of sequences. is there any perl code or some thing like this to do that? thanks a lot in advance

regards

[Neilfws]

By "header", you mean everything after the ">"? Or just some part of everything after the ">"? Or including the ">"? It's important to be specific since a lot of people misunderstand "header".

[Mohammad Reza Bakhtiarizadeh]

I just want everything after the ">". and i have to say that i am not familiar with perl and i want a perl code to run. if possible help me. thanks a lot. regards

[Michael]

err, why don't you just post your code then?

Answer 1

[Frédéric Mahé]

For perl code, you can visit http://www.bioperl.org/wiki/Main_Page. If you just want to extract the headers, on a Linux/Unix system, a simple grep "^>" myfile.fasta should work.

Answer 2

[Michael]

Why so complicated? ;) Only the header in a fasta file contains > so you can use grep :

grep -e ">" my.fasta

or awk to remove the >:

$ awk 'sub(/^>/, "")' 
>aksdjfljfd
aksdjfljfd

[Mohammad Reza Bakhtiarizadeh]

Thanks so much, but i am not familiar with perl code. i need a complete code to run it. if possible guide me more. thanks again

[Mohammad Reza Bakhtiarizadeh]

Thanks. I fixed my problem. regards

[Michael]

this is not perl, it's unix ;)

[bioinfo]

what about i want to extract the header and their belonging sequences?

[ursadhip]

$ awk 'sub(/^>/, "")' your_file.fasta > desired_headers.txt

This is a single-line code solution. No residual ">" before each header.

Learned from the blog "AWK: the substr command to select a substring" by Thomas Cokelaer

https://thomas-cokelaer.info/blog/2011/05/awk-the-substr-command-to-select-a-substring/

[Michael]

Yeah, sure, no rocket science ....

Answer 3

[Caddymob]

Expression in perl would be basically the same as the grep above (m/^>/).. There are easier 1-liner ways to do this, but this is a basic outline of the perl code that should be pretty readable.

#!/usr/bin/perl

open(FASTA, "<your.fa");
while(<FASTA>) {
    chomp($_);
    if ($_ =~  m/^>/ ) {
        my $header = $_;
        print "$header\n";
    }
}

[Mohammad Reza Bakhtiarizadeh]

thanks so much. your code is ok but how can i write it in a text file. i am not familiar with perl code.

thanks

[Mohammad Reza Bakhtiarizadeh]

thanks so much i fixed my problem. regards