NAME¶
Bio::Graphics::Browser2::GFFhelper -- Helps gbrowse plugins handle GFF
SYNOPSIS¶
package Bio::Graphics::Browser2::Plugin::MyPlugin;
use vars qw/@ISA $ROLLBACK/;
@ISA = qw/ Bio::Graphics::Browser2::Plugin
Bio::Graphics::Browser2::GFFhelper /;
$ROLLBACK = '/tmp/';
# other plugin subs skipped...
sub save_segment {
my ($self, $segment) = @_;
return 0 unless $ROLLBACK;
$self->{rb_loc} ||= $ROLLBACK;
$self->save_state($segment);
1;
}
sub gff_from_rollback {
my $self = shift;
my $conf = $self->configuration;
# don't save a persistent rb_id, look for a CGI param each time
my $rollback = $self->config_param('rb_id');
my $gff = $self->rollback($rollback);
# this is a rollback to an earlier version of an existing segment
# we don't need DNA, just the GFF
$gff;
}
# read GFF2 dialects
sub gff {
my $self = shift;
my $gff = shift;
# set a flag to add a header to the GFF
$self->{header} = 1;
# set sequence name in case the GFF does not have it
$self->refseq('L16622');
# process the GFF, convert it to GFF3, get the sequence
my ($newGFF, $dna) = $self->read_gff($gff);
return ($newGFF, $dna);
}
DESCRIPTION¶
This modules helps process GFF prior to loading into the database and provides
rollback capability for feature editors/loaders
GFF help¶
This module deals with the different GFF2 dialects and changes them to GFF3
format. It also allows conversion of Bio::DB::GFF::Feature objects to
Bio::SeqFeature::Generic objects, which is required for consistent feature and
attribute handling across different input/output formats.
If DNA is appended to the GFF, it will be extracted. The read_gff method returns
a string containing processed GFF and also a sequence string.
Rollbacks¶
The state of a segment can be captured and saved in case the user wishes to
revert to an earlier version of the segment after editing/deleting features.
The last 10 modified segments are saved in a round-robin rotation. In plugins
that inherit methods from this module, the $ROLLBACK
variable must be defined with a string containing the path to a directory
where the web user ('apache', 'nobody', etc.) has write access. If
$ROLLBACK is undefined, the rollback functionality is
disabled.
AUTHOR - Sheldon McKay¶
Email smckay@bcgsc.bc.ca
This package and its accompanying libraries is free software; you
can redistribute it and/or modify it under the terms of the GPL (either
version 1, or at your option, any later version) or the Artistic License
2.0. Refer to LICENSE for the full license text. In addition, please see
DISCLAIMER.txt for disclaimers of warranty.