NAME

Bio::WGS2NCBI::FeatureSet - container of sets of features

DESCRIPTION

Objects from this class maintain an internal set of all sequence features for a given sequence ID. Features can are added (or removed) from the set while Bio::WGS2NCBI is reading a sequence with its annotations. In addition, objects from this class maintain an (integer) offset by which all features are shifted, e.g. in the case where a scaffold starts with an assembly gap that needs to be removed. Lastly, objects from this class implement the logic for serializing all the annotations for a given sequence in feature table format.

METHODS

new()

Returns a new Bio::WGS2NCBI::FeatureSet object. This constructor has one required, named argument: 'seqid', which is the identifier of the sequence for which this set holds the features. In addition, optionally, an array reference of 'features' and an 'offset' can be provided. For example:

 my $set = Bio::WGS2NCBI::FeatureSet->new(
        seqid    => 'scaffold1.1',
        features => [ $feat1, $feat2 ],
        offset   => 33,
 );

offset()

Gets/sets the offset by which all feature coordinates must be shifted.

add()

Adds one or more features to the set.

remove()

Removes one or more features from the set.

to_string()

Writes the set out in feature table format.

read_feature_set

read_features

Reads and returns a FeatureSet. Arguments:

- the file handle to read from - a counter hash to generate IDs - the Config object - the focal Seq object - the offset at the start of the sequence (e.g. after leading NNNs) - the index of the last non-N residue in the sequence

write_features

Writes the FeatureSet to the provided file handle.