Lincoln D. Stein > GBrowse-2.55 > Bio::DB::GFF::Aggregator::reftranscript

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NAME ^

package Bio::DB::GFF::Aggregator::reftranscript -- Aggregates references transcripts

SYNOPSIS ^

use Bio::DB::GFF::Aggregator;

DESCRIPTION ^

Bio::DB::GFF::Aggregator::retranscript was written to make the compound feature, "reftranscript" for use with Gbrowse editing software developed outside of the GMOD development group. It can be used to aggregate "reftranscripts" from "refexons", loaded as second copy features. These features, in contrast to "transcripts", are usually implemented as features which cannot be edited and serve as starting point references for annotations added using Gbrowse for feature visualization.

Adding features to the compound feature, "reftranscript", can be done by adding to the "part_names" call (i.e. "refCDS").

method

 Title   : method
 Usage   : $aggregator->method
 Function: return the method for the composite object
 Returns : the string "reftranscript"
 Args    : none
 Status  : Public

part_names

 Title   : part_names
 Usage   : $aggregator->part_names
 Function: return the methods for the sub-parts
 Returns : the list "refexon"
 Args    : none
 Status  : Public

main_name

 Title   : main_name
 Usage   : $aggregator->main_name
 Function: return the method for the main component
 Returns : the string "reftranscript"
 Args    : none
 Status  : Public

BUGS ^

None reported.

SEE ALSO ^

Bio::DB::GFF, Bio::DB::GFF::Aggregator

AUTHOR ^

Paul Rudnick <rudnick@ncifcrf.gov>.

Copyright (c) 2002 Advanced Biomedical Computing Center, SAIC/NCI-Frederick.

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

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