Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
323 lines (251 sloc) 8.92 KB
#!/usr/bin/perl
#
# $Id: Coverage.pm,v 1.1 2002-10-23 21:43:19 mavcunha Exp $
#
#
=head1 NAME
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 TODO
Write some docs.
=head1 AUTHOR
Marco Valtas E<lt>mavcunha@bit.fmrp.usp.brE<gt>
Copyright (c) 2002 Regional Blood Center of Ribeirao Preto
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
=cut
package Bio::Graphics::Browser::Plugin::Coverage;
use strict;
use Bio::Graphics::Browser::Plugin;
use warnings;
use Carp;
use CGI qw(:standard *table);
use vars qw($VERSION @ISA);
@ISA = qw(Bio::Graphics::Browser::Plugin);
$VERSION = '0.10';
sub name { "Coverage" }
sub description {
p("This is a plugin to find the Coverage of a feature (query) in other feature (anchor).").
p(q[ Revision: $Revision: 1.1 $]).
p("Author: Marco Valtas (mavcunha\@bit.fmrp.usp.br)");
}
sub mime_type { "text/html"; }
sub type { 'dumper'; }
sub dump {
my ($self,$segment) = @_;
my $config = $self->configuration;
my $DEBUG = $config->{"debug"};# We are in debug mode?
# Checking some commom mistakes.
$self->_error('config',$segment) unless ($config->{query} and $config->{anchor});
# The multiple nature of query select turn check for same kind complicated.
#$self->_error('select',$segment) if ($config->{query} eq $config->{anchor});
if($DEBUG){
warn("===>Coverage Plugin Start ".localtime()." <===\n");
$self->_html_header("Coverage Plugin DEBUG Mode - ".localtime());
print "Segment requested: <b>$segment</b><br>";
print "User Configuration:<br>";
my $q = join(b(' and '),@{$config->{'query'}});
print "QUERY: <b>".$q."</b><br>";
print "ANCHOR:<b>".$config->{'anchor'}."</b><br>";
}
# Getting some more objects.
my $browser = $self->browser_config;
my $gff_db = $self->database;
my @query_feature;
push(@query_feature,$browser->label2type($_)) foreach @{$config->{'query'}};
my ($anchor_feature) = $browser->label2type($config->{'anchor'});
# what I got?
if($DEBUG){
print "Features:<br>";
print "QUERY FEATURE: <b>@query_feature</b><br>";
print "ANCHOR FEATURE: <b>$anchor_feature</b><br>";
}
my @anchors = $segment->features($anchor_feature);
my $total_q;
{
my %total_query;
$total_query{$_->name}++ foreach $segment->features(-type=>@query_feature);
$total_q = int(keys %total_query);
}
# We have found a anchor in the present segment?
$self->_error("noanchor",$segment) unless @anchors;
print "<br>Anchors found: <b>@anchors</b><br><br>" if $DEBUG;
my $total_anchors = $#anchors + 1;# How many anchors?
my %total_query_overlap;
my %total_anchor_overlap;
# if we are here, probably is alright, so let's begin the html.
$self->_html_header("Coverage Plugin - $segment ") unless $DEBUG;
my @table_fill; # This will keep the list of match, for later.
# Overlap block search.
print "Starting overlap search:<br>" if $DEBUG;
foreach my $anchor (@anchors){
my $a_seg = $gff_db->segment($anchor);
print "ANCHOR <b>$anchor</b> SEGMENT <b>$a_seg</b><BR>" if $DEBUG;
my @overlap = $a_seg->overlapping_features(@query_feature);# See Bio:DB::GFF
# Buffering our results.
push(@table_fill,td({-class=>'datatitle'},a({-href=>"gbrowse?name=".$anchor->name},$anchor->name)));
foreach my $match (@overlap){
$total_query_overlap{$match->name}++; # Count all query overlaps.
$total_anchor_overlap{$anchor}++; # Count overlaps by anchors
# Preparing the output table.
push(@table_fill,td({-class=>'databody'},$match->name));
print "->Overlap <b>$match</b><br>" if $DEBUG;
}
}
my $q = join(b(' and '),@{$config->{query}});
#We need a summary table.
print
table({-width=>'100%'},
TR({-class=>'searchtitle'},
td({-colspan=>'2',-align=>'center'},b("Summary of the Coverage"))
),
TR({-class=>'searchbody'},[
td(["Anchor Selected",$config->{anchor}]),
td(["Query Selected",$q]),
td(["Total of anchors in segment", $total_anchors]),
td(["Total of queries in segment", $total_q]),
td(["Total of overlapping queries", int(keys %total_query_overlap) ]),
td(["Total of anchors that had at least one overlap",int(keys %total_anchor_overlap)]),
td(["Percent of Coverage",sprintf("%.2f",((int(keys %total_anchor_overlap)/$total_anchors)*100))."%"]),
])
);
# Here is the list of features that matched, if the user marked
# show all matchs, this will displayed too.
if($config->{list_match}){
print
table({-width=>'100%'},
TR({-align=>'left'},
td({-class=>'datatitle',-align=>'center'},"List of the overlapping features")
),
TR({-align=>'left'},\@table_fill)
);
}
$self->_html_footer;
warn("===>Coverage Plugin End ".localtime()." <===\n") if $DEBUG;
return;
}
# Empty defaults.
sub config_defaults {
my $self = shift;
return { };
}
sub reconfigure {
my($self) = @_;
my $config = $self->configuration;
# Madatory configurations
# foreach my $option (@queries){
# push(@{$config->{'query'}},$option
# my @queries
$config->{'query'} = [param('Coverage.query')];
$config->{'anchor'} = param('Coverage.anchor');
# Optional configuration.
# This configuration lists all matches.
$config->{'list_match'} = param('Coverage.list_match');
# Debug mode checkbox.
$config->{'debug'} = param('Coverage.debug');
return;
}
sub configure_form {
my ($self) = @_;
my $b = $self->browser_config;
my $config = $self->configuration;
return
table({-width=>'100%'},
TR({-class=>'searchtitle'},
th({-colspan=>'3',-align=>'LEFT'},
"Enter the configuration.",
)
),
TR({-class=>'searchbody','-align'=>'left'},
td(b('Query<br>'),
checkbox_group('-name'=>"Coverage.query",
-values=>[$b->labels],
-linebreak=>'true',
-default=>\@{$config->{query}},
),
td({-valign=>'top'},b('Anchor<br>'),
radio_group('-name'=>"Coverage.anchor",
-values=>[$b->labels],
-linebreak=>'true',
-default=>$config->{anchor},
),
),
td({-valign=>'top'},b('Options<br>'),
checkbox(-name=>'Coverage.list_match',
-value=>'1',
-label=>'Show match list'),'<br>',
#checkbox(-name=>'Coverage.debug',
# -value=>'1',
# -label=>'Turn on debug'),
),
),
)
);
}
sub _error {
my($self,$error_key,$segment) = @_;
my $config = $self->configuration;
# Error messages
my %error_message = (
"noanchor" =>
p("Can not find a anchor ",
font({-color=>'red'},$config->{anchor}),
" in this segment ",
font({-color=>'red'},$segment)
),
"config" =>
p("Missing configuration, use ",
font({-color=>'red'},"Configure"),
" before hit ",
font({-color=>'red'},"Go!")
),
"select" =>
p("You selected the same feature ",
font({-color=>'red'},$config->{query}),
" in both boxes, please select different
features. Hit \"Back\" on your Browser"
),
);
# Now we print out the error to the user.
print
$self->_html_header('Coverage Plugin Error'),
table({-width=>'100%'},
TR({-class=>'datatitle'},
td({-colspan=>'2',-align=>'LEFT'},
"An error occured in your request",
)
),
TR({-class=>'databody'},
td({-colspan=>'2',-align=>'LEFT'},
$error_message{$error_key},
)
),
);
$self->_html_footer; # the end.
exit(0);
}
sub _html_header {
my($self,$title) = @_;
my $browser = $self->browser_config;
print
start_html(-title =>$title,
-style => {src=>$browser->setting('stylesheet')},
),h1($title);
return;
}
sub _html_footer {
my($self) = @_;
print
table({-width=>'100%'},
th(
p({-align=>'left'},"Author: ",
a({-href=>'mailto:mavcunha@bit.fmrp.usp.br'},"Marco Valtas (mavcunha\@bit.fmrp.usp.br) ").
localtime()
),
)
).
end_html;
return;
}
1;
You can’t perform that action at this time.