#
# BioPerl module for Bio::Tools::tRNAscanSE
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output
=head1 SYNOPSIS
use Bio::Tools::tRNAscanSE;
my $parser = Bio::Tools::tRNAscanSE->new(-file => 'result.tRNAscanSE');
# parse the results
while( my $gene = $parser->next_prediction ) {
@exon_arr = $gene->get_SeqFeatures();
}
=head1 DESCRIPTION
This script will parse tRNAscan-SE output. Just the tabular output of
the tRNA locations in the genome for now.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::tRNAscanSE;
use strict;
use Bio::SeqFeature::Generic;
use base qw(Bio::Tools::AnalysisResult);
use vars qw($GeneTag $SrcTag $ExonTag);
($GeneTag,$SrcTag,$ExonTag) = qw(gene tRNAscan-SE exon);
=head2 new
Title : new
Usage : my $obj = Bio::Tools::tRNAscanSE->new();
Function: Builds a new Bio::Tools::tRNAscanSE object
Returns : an instance of Bio::Tools::tRNAscanSE
Args : -fh/-file for input filename
-genetag => primary tag used in gene features (default 'tRNA_gene')
-exontag => primary tag used in exon features (default 'tRNA_exon')
-srctag => source tag used in all features (default 'tRNAscan-SE')
=cut
sub _initialize {
my($self,@args) = @_;
$self->SUPER::_initialize(@args);
my ($genetag,$exontag,$srctag) = $self->SUPER::_rearrange([qw(GENETAG
SRCTAG
EXONTAG)],
@args);
$self->gene_tag(defined $genetag ? $genetag : $GeneTag);
$self->source_tag(defined $srctag ? $srctag : $SrcTag);
$self->exon_tag(defined $exontag ? $exontag : $ExonTag);
$self->{'_seen'} = {};
}
=head2 gene_tag
Title : gene_tag
Usage : $obj->gene_tag($newval)
Function: Get/Set the value used for the 'gene_tag' of genes
Default is 'tRNA_gene' as set by the global $GeneTag
Returns : value of gene_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub gene_tag{
my $self = shift;
return $self->{'gene_tag'} = shift if @_;
return $self->{'gene_tag'};
}
=head2 source_tag
Title : source_tag
Usage : $obj->source_tag($newval)
Function: Get/Set the value used for the 'source_tag' of exons and genes
Default is 'tRNAscan-SE' as set by the global $SrcTag
Returns : value of source_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub source_tag{
my $self = shift;
return $self->{'_source_tag'} = shift if @_;
return $self->{'_source_tag'};
}
=head2 exon_tag
Title : exon_tag
Usage : $obj->exon_tag($newval)
Function: Get/Set the value used for the 'primary_tag' of exons
Default is 'tRNA_exon' as set by the global $ExonTag
Returns : value of exon_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub exon_tag{
my $self = shift;
return $self->{'_exon_tag'} = shift if @_;
return $self->{'_exon_tag'};
}
=head2 analysis_method
Usage : $genscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/tRNAscan-SE/i.
Returns : String
Argument : n/a
=cut
#-------------
sub analysis_method {
#-------------
my ($self, $method) = @_;
if($method && ($method !~ /tRNAscan-SE/i)) {
$self->throw("method $method not supported in " . ref($self));
}
return $self->SUPER::analysis_method($method);
}
=head2 next_feature
Title : next_feature
Usage : while($gene = $genscan->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Genscan result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::SeqFeature::Generic object.
Args :
See also : L<Bio::SeqFeature::Generic>
=cut
sub next_feature {
my ($self,@args) = @_;
# even though next_prediction doesn't expect any args (and this method
# does neither), we pass on args in order to be prepared if this changes
# ever
return $self->next_prediction(@args);
}
=head2 next_prediction
Title : next_prediction
Usage : while($gene = $genscan->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the Genscan result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : A Bio::SeqFeature::Generic object.
Args :
See also : L<Bio::SeqFeature::Generic>
=cut
sub next_prediction {
my ($self) = @_;
my ($genetag,$srctag,$exontag) = ( $self->gene_tag,
$self->source_tag,
$self->exon_tag);
while( defined($_ = $self->_readline) ) {
if( m/^(\S+)\s+ # sequence name
(\d+)\s+ # tRNA #
(\d+)\s+(\d+)\s+ # tRNA start,end
(\w{3})\s+ # tRNA type
([CAGT]{3})\s+ # Codon
(\d+)\s+(\d+)\s+ # Intron Begin End
(\d+\.\d+)/ox # Cove Score
) {
my ($seqid,$tRNAnum,$start,$end,$type,
$codon,$intron_start,$intron_end,
$score) = ($1,$2,$3,$4,$5,$6,$7,$8,$9);
my $strand = 1;
if( $start > $end ) {
($start,$end,$strand) = ($end,$start,-1);
}
if( $self->{'_seen'}->{$type}++ ) {
$type .= "-".$self->{'_seen'}->{$type};
}
my $gene = Bio::SeqFeature::Generic->new
( -seq_id => $seqid,
-start => $start,
-end => $end,
-strand => $strand,
-score => $score,
-primary_tag => $genetag,
-source_tag => $srctag,
-tag => {
'ID' => "tRNA:$type",
'Name' => "tRNA:$type",
'AminoAcid' => $type,
'Codon' => $codon,
});
if( $intron_start ) {
if( $intron_start > $intron_end ) {
($intron_start,$intron_end) = ($intron_end,$intron_start);
}
$gene->add_SeqFeature(Bio::SeqFeature::Generic->new
( -seq_id=> $seqid,
-start => $start,
-end => $intron_start-1,
-strand=> $strand,
-primary_tag => $exontag,
-source_tag => $srctag,
-tag => {
'Parent' => "tRNA:$type",
}));
$gene->add_SeqFeature(Bio::SeqFeature::Generic->new
( -seq_id=> $seqid,
-start => $intron_end+1,
-end => $end,
-strand=> $strand,
-primary_tag => $exontag,
-source_tag => $srctag,
-tag => {
'Parent' => "tRNA:$type"
}));
} else {
$gene->add_SeqFeature(Bio::SeqFeature::Generic->new
( -seq_id=> $seqid,
-start => $start,
-end => $end,
-strand=> $strand,
-primary_tag => $exontag,
-source_tag => $srctag,
-tag => {
'Parent' => "tRNA:$type"
}));
}
return $gene;
}
}
}
1;