#!/usr/bin/perl
use warnings;
use strict;

my $previous_gn = "";
my $header;
while (<>) {
    if (my ($gn) = /^>.* GN=([^ ]+)/) {
        if ($gn ne $previous_gn) {
            $previous_gn = $gn;
            $header = $_;
        }
    } else {
        if ($header) {
            print $header, $_;
            undef $header;
        }
    }
}
[download]

If the header with the same GN don't have to be consecutive, you need to remember all the GN's seen so far. A hash is the best structure to remember them:

#!/usr/bin/perl
use warnings;
use strict;

my %seen;
my $header;
my $gn;
while (<>) {
    if (/^>.* GN=([^ ]+)/) {
        $gn = $1;
        $header = exists $seen{$gn} ? undef : $_;
    } elsif ($header) {
        undef $seen{$gn};
        print $header, $_;
    }
}
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For example, something along these lines (untested):

my %seen;
while (my $line = <$IN>) {
    my $gn = $1 if $line =~ / GN=(\w+) /;
    next if exists $seen{$1};
    $seen{$1} = 1;
    print $line;
}
[download]

Otherwise, if that doesn't help, I agree with 1nickt: please show the code that you have, it will be much easier to help you.

Hi, welcome! There's lots of help here. The thing to do is show what you have, what works, what doesn't, what error messages you are getting. See SSCCE. Like, can you open the file yet? Can you read a line from it yet? And so on.

Sorry, I should have mentioned this. But, actually I'm new to perl. I thought of asking you guys to have some kind of knowledge and then kind of start learning from there.

How new? :-) If you have not yet, set aside an afternoon and go through perlintro. There's a section there for virtually each piece of what you need to do in your program. Start with some simple exercises, loops, etc. Don't try to pull off your goal in the first step. See my follow up to the code you showed here.



The way forward always starts with a minimal test.

#!/usr/bin/perl
use warnings;
use strict;

print 'Enter protein sequence filename: ';
chomp( my $prot_filename = <STDIN> );

open my $PROTFILE, '<', $prot_filename
  or die "Cannot open '$prot_filename' because: $!";

my $out_filename = 'duplicate_gene_entries_in_'.$prot_filename;
open my $OUTFILE, '>', $out_filename
  or die "Cannot open '$out_filename' because: $!";

$/ = ''; # Set paragraph mode


my %seen;
my $header;
my $count_in;
my $count_out;
my $gn;
while (<>) {
    if (/^>.* GN=([^ ]+)/) {
        $gn = $1;
        $header = exists $seen{$gn} ? undef : $_;
    } elsif ($header) {
        undef $seen{$gn};
        print $header, $_;
    }
}
close $OUTFILE;
close $PROTFILE;
printf "%d total records read from '%s'\n",$count_in,$prot_filename;
printf "%d records written to '%s' after removing duplicate entries\n"
+,$count_out,$out_filename;
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This:

while (<>) {
[download]

is wrong, because you assigned a file handler to your input file. So, this should be:

while (<$PROTFILE>) {
[download]

Otherwise, I am not sure why you want to set to paragraph mode.

There may be some other problems, but that should help you to get going.

I want to set to paragraph mode because each of my entries is multiple lines long and is separated by a new line. So, I was reading about perl, it said I can use the paragraph mode to specify that. As I said, I'm new and still learning, let me know if it's wrong. Also, when I ran the code after correcting what you suggested, it gave me the following errors:

Use of uninitialized value $count_in in printf at ../remove_duplicate_genes.pl line 34.

0 total records read from 'enzymes.fasta'

Use of uninitialized value $count_out in printf at ../remove_duplicate_genes.pl line 35.

0 records written to 'duplicate_gene_entries_in_enzymes.fasta' after removing duplicate entries