| Bio::Tools::tRNAscanSE(3pm) | User Contributed Perl Documentation | Bio::Tools::tRNAscanSE(3pm) |
Bio::Tools::tRNAscanSE - A parser for tRNAscan-SE output
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();
}
This script will parse tRNAscan-SE output. Just the tabular output of the tRNA locations in the genome for now.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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')
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)
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)
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)
Usage : $genscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/tRNAscan-SE/i.
Returns : String
Argument : n/a
Title : next_feature
Usage : while($gene = $genscan->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the Genscan result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::SeqFeature::Generic object.
Args :
See also : L<Bio::SeqFeature::Generic>
Title : next_prediction
Usage : while($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>
| 2021-08-15 | perl v5.32.1 |