Gono has asked for the wisdom of the Perl Monks concerning the following question:

Hi monks, by using the following code, I want printed data to be displayed in the text box...but all that I get within the textbox is the following: Bio::SeqFeature::Generic=HASH(0x6547e0), etc. Please Help! 


Many thanks!

Code:

#! /usr/local/bin/perl -wT

use strict;
use CGI qw / :standard /;
use CGI::Pretty;
use Bio::SeqIO;
use Bio::Root::IO;
use Bio::SeqFeature::Generic;
use Bio::Location::Simple;
use Bio::Location::SplitLocationI;
use File::Temp;

my @features = read_file(param('file'));

print header, start_html('Plasmid Feature Editor');

print h1('Plasmid Feature Editor');

print p('Load up a Genbank file to work with, then edit the features i
+n the text box.');

print <<END;
<BODY BGCOLOR = "#ffffcc">
END

print start_multipart_form(),
  table({-cellpadding => 10},
    TR({-class=> 'resultsbody'},
       td(textarea(-name     => 'editarea',
               -value    => "@features",
               -rows     => 20,
               -cols     => 70,
               -override => (@features) || (param('clear')),
               ),
         ),
      ),
    TR({-class=>'resultstitle'},
       td(filefield(-name    => 'file',
            -length  => 40),
         ),
       td(submit(-name  => 'submit_button',
             -value => 'Click to display features'),
         ),
      ),
    TR({-class=>'resultstitle'},
       td(submit(-name  => 'save_button',
             -value => 'Click here to save your work'),
         ),
       td(reset(),
         ),
      ),
       ),
  end_form;

print <<FINISH;
</BODY>
FINISH

print end_html;

exit 0;

sub read_file {

my $fh = param('file'); 
my $gb_parser = Bio::SeqIO->new(-fh=>$fh,-format=>'Genbank'); 
my @features; 
while (my $seq = $gb_parser->next_seq) { 
    push @features, $seq->get_all_SeqFeatures(); 
} return @features; 
}

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Edited by Chady -- added code tags.

Replies are listed 'Best First'.
Re: Displaying data?
by Happy-the-monk (Canon) on Mar 10, 2004 at 18:50 UTC

    it seems that where you do the
    push @features, $seq->get_all_SeqFeatures();
    part, you are pushing a hash reference onto the array, but you thought it was some string data.

    you should find out:

    use Data::Dumper; # goes somewhere at the top of the script. then...
print Dumper \@features; # goes right before the return @features;stat
+ement.

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