---
name: "Bio::DB::GFF::Aggregator::clone"
section: "3pm"
platform: "linux"
package: "libbio-db-gff-perl"
version: "1.7.4-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::DB::GFF::Aggregator::clone"
---

# Bio::DB::GFF::Aggregator::clone(3pm)

## NAME

Bio::DB::GFF::Aggregator::clone -- Clone aggregator

## SYNOPSIS

```
  use Bio::DB::GFF;
  # Open the sequence database
  my $db      = Bio::DB::GFF->new( -adaptor => 'dbi:mysql',
                                   -dsn     => 'dbi:mysql:elegans42',
                                   -aggregator => ['transcript','clone'],
                                 );
 ----------------------------------------------------------------------------
 Aggregator method: clone
 Main method:       -none-
 Sub methods:       Clone_left_end Clone_right_end region:Genomic_canonical
 ----------------------------------------------------------------------------
```

## DESCRIPTION

Bio::DB::GFF::Aggregator::clone is one of the default aggregators, and was written to be compatible with the C elegans GFF files.  It aggregates raw "Clone\_left\_end", "Clone\_right\_end", and "region:Genomic\_canonical" features into composite features of type "clone".

### aggregate

```
 Title   : aggregate
 Usage   : $features = $a->aggregate($features,$factory)
 Function: aggregate a feature list into composite features
 Returns : an array reference containing modified features
 Args    : see L<Bio::DB::GFF::Aggregator>
 Status  : Public
```

The WormBase GFF model is unusual in that clones aren't identified as a single feature with start and stop positions, but as two features, a "left end" and a "right end".  One or both of these features may be absent.  In order to accommodate this, the aggregator will return undef for the start and/or stop if one or both of the ends are missing.

### method

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

### part\_names

```
 Title   : part_names
 Usage   : $aggregator->part_names
 Function: return the methods for the sub-parts
 Returns : the list ("Clone_left_end", "Clone_right_end", "region:Genomic_canonical")
 Args    : none
 Status  : Public
```

## BUGS

None reported.

## SEE ALSO

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

## AUTHOR

Lincoln Stein \<lstein@cshl.org\>.

Copyright (c) 2001 Cold Spring Harbor Laboratory.

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