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Bio::DB::GFF::Feature 1.4
Bio::DB::GFF::Feature is a relative segment identified by a feature type. more>>
Bio::DB::GFF::Feature is a relative segment identified by a feature type.
Bio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed).
Bio::DB::GFF::Feature adds new methods to retrieve the annotations type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file.
Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class.
Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules.
Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment->features() method.
Important note about start() vs end()
If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points.
To avoid this behavior, call $segment->absolute(1) before fetching features from it. This will force everything into absolute coordinates.
For example:
my $segment = $db->segment(CHROMOSOME_I);
$segment->absolute(1);
my @features = $segment->features(transcript);
<<lessBio::DB::GFF::Feature is a stretch of sequence that corresponding to a single annotation in a GFF database. It inherits from Bio::DB::GFF::RelSegment, and so has all the support for relative addressing of this class and its ancestors. It also inherits from Bio::SeqFeatureI and so has the familiar start(), stop(), primary_tag() and location() methods (it implements Bio::LocationI too, if needed).
Bio::DB::GFF::Feature adds new methods to retrieve the annotations type, group, and other GFF attributes. Annotation types are represented by Bio::DB::GFF::Typename objects, a simple class that has two methods called method() and source(). These correspond to the method and source fields of a GFF file.
Annotation groups serve the dual purpose of giving the annotation a human-readable name, and providing higher-order groupings of subfeatures into features. The groups returned by this module are objects of the Bio::DB::GFF::Featname class.
Bio::DB::GFF::Feature inherits from and implements the abstract methods of Bio::SeqFeatureI, allowing it to interoperate with other Bioperl modules.
Generally, you will not create or manipulate Bio::DB::GFF::Feature objects directly, but use those that are returned by the Bio::DB::GFF::RelSegment->features() method.
Important note about start() vs end()
If features are derived from segments that use relative addressing (which is the default), then start() will be less than end() if the feature is on the opposite strand from the reference sequence. This breaks Bio::SeqI compliance, but is necessary to avoid having the real genomic locations designated by start() and end() swap places when changing reference points.
To avoid this behavior, call $segment->absolute(1) before fetching features from it. This will force everything into absolute coordinates.
For example:
my $segment = $db->segment(CHROMOSOME_I);
$segment->absolute(1);
my @features = $segment->features(transcript);
Download (4.7MB)
Added: 2006-06-09 License: Perl Artistic License Price:
1232 downloads
Bio::Graphics::FeatureFile 1.4
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file. more>>
Bio::Graphics::FeatureFile is a set of Bio::Graphics features, stored in a file.
SYNOPSIS
use Bio::Graphics::FeatureFile;
my $data = Bio::Graphics::FeatureFile->new(-file => features.txt);
# create a new panel and render contents of the file onto it
my $panel = $data->new_panel;
my $tracks_rendered = $data->render($panel);
# or do it all in one step
my ($tracks_rendered,$panel) = $data->render;
# for more control, render tracks individually
my @feature_types = $data->types;
for my $type (@feature_types) {
my $features = $data->features($type);
my %options = $data->style($type);
$panel->add_track($features,%options); # assuming we have a Bio::Graphics::Panel
}
# get individual settings
my $est_fg_color = $data->setting(EST => fgcolor);
# or create the FeatureFile by hand
# add a type
$data->add_type(EST => {fgcolor=>blue,height=>12});
# add a feature
my $feature = Bio::Graphics::Feature->new(
# params
); # or some other SeqI
$data->add_feature($feature=>EST);
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.
This moduel is a precursor of Jason Stajichs Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.
<<lessSYNOPSIS
use Bio::Graphics::FeatureFile;
my $data = Bio::Graphics::FeatureFile->new(-file => features.txt);
# create a new panel and render contents of the file onto it
my $panel = $data->new_panel;
my $tracks_rendered = $data->render($panel);
# or do it all in one step
my ($tracks_rendered,$panel) = $data->render;
# for more control, render tracks individually
my @feature_types = $data->types;
for my $type (@feature_types) {
my $features = $data->features($type);
my %options = $data->style($type);
$panel->add_track($features,%options); # assuming we have a Bio::Graphics::Panel
}
# get individual settings
my $est_fg_color = $data->setting(EST => fgcolor);
# or create the FeatureFile by hand
# add a type
$data->add_type(EST => {fgcolor=>blue,height=>12});
# add a feature
my $feature = Bio::Graphics::Feature->new(
# params
); # or some other SeqI
$data->add_feature($feature=>EST);
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you can interrogate it for its consistuent features and their settings, or render the entire file onto a Bio::Graphics::Panel.
This moduel is a precursor of Jason Stajichs Bio::Annotation::Collection class, and fulfills a similar function of storing a collection of sequence features. However, it also stores rendering information about the features, and does not currently follow the CollectionI interface.
Download (4.7MB)
Added: 2006-06-12 License: Perl Artistic License Price:
1229 downloads
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