Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output

SYNOPSIS

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   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();

   }

DESCRIPTION

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This script will parse tRNAscan-SE output. Just the tabular output of the tRNA locations in the genome for now.

FEEDBACK

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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

Support

Please direct usage questions or support issues to the mailing list:

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.

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/

AUTHOR - Jason Stajich

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Email jason-at-bioperl.org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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')

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)

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)

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)

analysis_method

 Usage     : $genscan->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /tRNAscan-SE/i.
 Returns   : String
 Argument  : n/a

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>

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>
BioPerl documentation Contained in the BioPerl distribution. 
#
# 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



# 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);


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'} = {};
}


sub gene_tag{
    my $self = shift;

    return $self->{'gene_tag'} = shift if @_;
    return $self->{'gene_tag'};
}


sub source_tag{
    my $self = shift;

    return $self->{'_source_tag'} = shift if @_;
    return $self->{'_source_tag'};
}


sub exon_tag{
    my $self = shift;

    return $self->{'_exon_tag'} = shift if @_;
    return $self->{'_exon_tag'};
}



#-------------
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);
}


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);
}


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;