[Bioperl-l] Parsing features

[Jonathon Greenwood]

I tried some of the code in the Feature Annotation HOWTO but it wouldn't
display anything within the text box.

Jonathan

On Fri, 12 Mar 2004, Jason Stajich wrote:

> Did you try some of the code in the Feature-Annotation HOWTO?
>   http://bioperl.org/HOWTOs/
>
> -jason
> On Fri, 12 Mar 2004, Jonathon Greenwood wrote:
>
> > Hi all!
> >
> > I'm wondering if it is possible to extract the features from a Genbank
> > file and print out the feature information within a text box (I'm dealing
> > with the text of the feature I don't want to display them as a glyph). I
> > tried this already using the Dumper method...but it spews out too much
> > information. I also get the errors when I run the code(which is for this
> > feature):
> > Bio::SeqFeature::Generic=HASH(0x654788) a bunch of times... and
> > (in cleanup) Undefined subroutine Fh:flush at
> > /usr/local/lib/perl5/site_perl/5.8.0/Bio/Root/IO.pm line 519
> >
> > Thanks for any help that can be given...
> >
> > Jonathan Greenwood
> > Co-op student,
> > email: jonathon at mgcheo.med.uottawa.ca
> >
> > CODE:
> >
> > #! /usr/local/bin/perl -w
> >
> > use strict;
> > use CGI qw / :standard /;
> > use CGI::Pretty;
> > use Bio::SeqFeature::Generic;
> > use Bio::SeqIO;
> > use Bio::Root::IO;
> > use File::Temp;
> >
> > my @features = read_file(param('file'));
> >
> > print header, start_html('Plasmid Feature Editor');
> >
> > print start_multipart_form (),
> > table ({-cellpadding => 10},
> > TR({-class => 'resultsbody'},
> > 	td (textarea(-name => 'editarea',
> > 		     -values => "@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 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_SeqFeatures();
> > }
> > return @features;
> > }
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
>