++ed by:

1 PAUSE user

Robert Buels
and 1 contributors


Bio::GFF3::Transform::SyncDirectives - insert sync (###) directives into an existing GFF3 file. WARNING: this module does not really work in the general case, read the DESCRIPTION section below.


    use Bio::GFF3::Transform::SyncDirectives 'gff3_add_sync_directives';

    my @input_files = ( 'input1.gff3', 'input2.gff3' );
    open my $output_fh, '>', 'myoutputfile.gff3';
    gff3_add_sync_directives( $output_fh, @input_files );


This module, and its gff3_insert_sync_directives script, have some important caveats: they do not support Derives_from, they will not work if any child features come in the file before their parent (which in practice is unusual), and they do not work when more than one feature line has the same ID. Perhaps in the future I may get around to writing a more capable version of this.


All functions below are EXPORT_OK.

gff3_add_sync_directives( $out_filehandle, @files )

Read GFF3 from the given files, add as many sync directives (###) as possible, and print the resulting GFF3 to the given output filehandle. Existing sync directives will not be preserved.


Robert Buels <rmb32@cornell.edu>


This software is copyright (c) 2012 by Robert Buels.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.