How to Parse/Edit FASTA header

Imagine a situation that you have thousands of FASTA sequences in a file and want to shorten or edit the FASTA header instead of whole long unnecessary information.

1. You can also parse FASTA header using PERL scripts. Some are given below. 

headerparser-1.pl     DOWNLOAD

#!/bin/env perl
while (<>) {
  s/\s.*/\n/;
  print;
}

Uses

headerparser-2.pl input.txt

headerparser-2.pl     DOWNLOAD

#!/bin/env perl
while (<>) {
  if (/^(>\S+)/) {
    print "$1\n";
  } else {
    print;
  }
}

Uses

headerparser-1.pl input.txt

headerparser-3.pl     DOWNLOAD

#!/usr/bin/perl

use strict;
use warnings;
use Bio::SeqIO;




=head1 Synopsis



Input header >gi|120419786|gb|EH270482.2|EH270482 Gp_mxAA_21G01_M13R mxA Gammarus pulex cDNA clone Gp_mxAA_21G01 5', mRNA sequence

Output header >gi120419786 



=cut

unless (@ARGV ==1){ die "Usage:  shortenIDs.pl  fastaFileName";} 

my $origFile = shift;  
my $newFile=$origFile . ".txt";

my $seq_in  = Bio::SeqIO->new( -format => 'fasta',
                                   -file => $origFile);

my $seq;
my $seq_out = Bio::SeqIO->new('-file' => ">$newFile",
                                       '-format' => 'fasta');

while( $seq = $seq_in->next_seq() ) 
{
 my $seqName = $seq->id;
  $seqName =~ s/\|/\./g; #replace pipe with dot
        $seqName =~ s/(gi)\.(\w*)\..*/$1$2/;  
 #my $desc = $seq->description;
        $seq->id($seqName);
 $seq->description("");
 
 $seq_out->write_seq($seq);
}

print "Your sequences have been renamed and are in the file $newFile\n\n";

Uses

headerparser-3.pl input.txt

Dependencies

This FASTA header PERL script required Bio::SeqIO; for proper functioning.