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

my %info; # here we collect all information
my @columns = qw(gi version cds); # The name and order of the columns 
+we want to print

my $data = '/DATA/GenBankFile.gb'; # GenBank file is located at C:\DAT
+A
open INFILE, '<', $data or die "Cannot open file!\n";

while (<INFILE>) {
    if (m!GI:(\d+)!) {
        if ($info{cds}) { # we are in a CDS block
            $info{gi} = $1;
        };
    } elsif (m!^\s+CDS\s+(.*)!) {
        # a new gene information has started
        flush_info();

        # now remember the CDS
        $info{cds} = $1
    } elsif (m!^VERSION.*\w:(\d+)! ) {
        $info{ version } = $1;
    } else {
        warn "Ignoring unknown line [$_]\n";
    };
};

# Output any leftover information:
flush_info();

sub flush_info {
    # print out all information:
    print join '*', @info{@columns}; #Line 34

    # and forget the collected information
    %info = ();
};
[download]

Nowhere in that source code does the word value appear, so I highly doubt that the program ever outputs the string Ignoring unknown value. I put the following line into the program:

warn "Ignoring unknown line [$_]\n";
[download]

in there so you know what parts of the input get discarded. In that line, I even output the part that gets discarded. If you determine that a certain line is never of use, just add another rule ignoring it.

So I turned off the warnings

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

my %info; # here we collect all information
my @columns = qw(gi version cds); # The name and order of the columns 
+we want to print

my $data = '/PRBB/Practice.gb'; # GenBank file is located at C:\PRBB
open INFILE, '<', $data or die "Please insert a new coin!\n";

while (<INFILE>) {
    if (m!GI:(\d+)!) {
        if ($info{cds}) { # we are in a CDS block
            $info{gi} = $1;
        };
    } elsif (m!^\s+CDS\s+(.*)!) {
        # a new gene information has started
        flush_info();

        # now remember the CDS
        $info{cds} = $1
    } elsif (m!^VERSION.*\w:(\d+)! ) {
        $info{ version } = $1;
    #} else {warn "Ignoring unknown line [$_]\n";};
};}

# Output any leftover information:
flush_info();

sub flush_info {
    # print out all information:
    print join '*', @info{@columns};

    # and forget the collected information
    %info = ();
};
[download]

This gives an error at print join '*', @info{@columns}; And it prints all the matchings into one single line. How is it possible to print them out as would be in the following structure:

if ( defined $cds && defined $gi && defined $version ) { # Print only 
+when all variables are defined
        print "$gi\t$version\t$cds\n";
        $gi = $cds = undef; # Get ready for the next loop
        }
[download]

Thanks for sparing time!