Raw content of Bio::SearchIO::chado
<![CDATA[# $Id: chado.pm,v 1.1 2002/12/03 08:13:55 cjm Exp $
#
# BioPerl module for Bio::SearchIO::chado
#
# Chris Mungall <cjm@fruitfly.org>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::SearchIO::chado - chado sequence input/output stream
=head1 SYNOPSIS
It is probably best not to use this object directly, but
rather go through the SearchIO handler system. Go:
$stream = Bio::SearchIO->new(-file => $filename, -format => 'chado');
while ( my $seq = $stream->next_seq() ) {
# do something with $seq
}
=head1 DESCRIPTION
This object can transform Bio::Seq objects to and from chado flat
file databases. CURRENTLY ONLY TO
=head2 Optional functions
=over 3
=item _show_dna()
(output only) shows the dna or not
=item _post_sort()
(output only) provides a sorting func which is applied to the FTHelpers
before printing
=back
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://www.bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/
=head1 AUTHOR - Chris Mungall
Email cjm@fruitfly.org
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::SearchIO::chado;
use vars qw(@ISA);
use strict;
use Bio::SearchIO;
use Bio::SeqFeature::Generic;
use Bio::Seq::SeqFactory;
use Bio::Annotation::Collection;
use Bio::Annotation::Comment;
use Bio::Annotation::Reference;
use Bio::Annotation::DBLink;
use Bio::SeqIO::chado;
use Data::Stag qw(:all);
# should really inherit off of a chado helper...
@ISA = qw(Bio::SearchIO Bio::SeqIO::chado);
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
my $wclass = $self->default_handler_class;
$self->handler($wclass->new);
$self->{_end_of_data} = 0;
$self->handler->S("chado");
return;
}
sub DESTROY {
my $self = shift;
$self->end_of_data();
$self->SUPER::DESTROY();
}
sub end_of_data {
my $self = shift;
$self->{_end_of_data} = 1;
$self->handler->E("chado");
}
sub default_handler_class {
return "Data::Stag::BaseHandler";
}
=head2 write_result
Title : write_result
Usage : $stream->write_result($result)
Function: writes the $result object (must be result) to the stream
Returns : 1 for success and 0 for error
Args : Bio::Result
=cut
sub write_result {
my ($self,$result) = @_;
if( !defined $result ) {
$self->throw("Attempting to write with no result!");
}
my $w = $self->handler;
$w->S("result");
# my $result_temp_uid = $self->get_temp_uid($result);
my @stats =
(map {
[analysisprop=>[
[pkey=>$_],
[pval=>$result->get_statistic($_)]]]
} $result->available_statistics);
my @params =
(map {
[analysisprop=>[
[pkey=>$_],
[pval=>$result->get_parameter($_)]]]
} $result->available_parameters);
my $cid = $self->get_temp_uid($result);
$w->ev(companalysis=>[
[companalysis_id=>$cid],
[datasource=>$result->database_name],
@stats,
@params,
]
);
while( my $hit = $result->next_hit ) {
# process the Bio::Search::Hit::HitI object
$self->write_hit($hit, $cid);
}
$w->E("result");
return 1;
}
sub write_hit {
my $self = shift;
my $hit = shift;
my $cid = shift;
my $w = $self->handler;
my $hit_id = $self->get_temp_uid($hit);
# we should determine the type by the type of blast;
# eg blastx gives CDS for hit and CDS_exon for HSP
my $fnode =
[feature=> [
[feature_id=>$hit_id],
[name=>$hit->name],
[typename=>"hit"],
[analysisfeature=>[
[rawscore=>$hit->raw_score],
[significance=>$hit->significance],
[analysis_id=>$cid]]]]];
$w->ev(@$fnode);
foreach my $hsp ( $hit->hsps) {
$self->write_hsp($hsp, $hit_id);
}
return 1;
}
sub write_hsp {
my $self = shift;
my $hsp = shift;
my $hid = shift;
my $w = $self->handler;
my $hsp_id = $self->get_temp_uid($hsp);
my $order = 0;
my @lnodes =
map {
my ($nbeg, $nend, $strand) =
$self->bp2ib([$hsp->start($_),
$hsp->end($_),
$hsp->strand($_)
]);
my $src = $_ eq 'query' ? $hsp->query->seq_id : $hsp->hit->seq_id;
[featureloc=>[
[nbeg=>$nbeg],
[nend=>$nend],
[strand=>$strand],
[srcfeature=>$src],
[group=>0],
[order=>$order++],
]
]
} qw(query subject);
my $fnode =
[feature => [
[feature_id=>$hsp_id],
[typename=>"hsp"],
[analysisfeature=>[
[rawscore=>$hsp->score],
[significance=>$hsp->significance],
]
],
@lnodes,
]
];
$w->ev(@$fnode);
$w->ev(feature_relationship=>[
[subjfeature_id=>$hsp_id],
[objfeature_id=>$hid]
]
);
return 1;
}
1;
]]>