iPE::Annotation::Transcript(3)

NAME
iPE::Annotation::Transcript - A state sequence representing the features of a transcript.

DESCRIPTION
This is an object created by iPE::AnnotationPlugin upon reading in the Annotation file and translating the features to iPE::Annotation::Features via iPE::Annotation::FeatureMappings. These presumably contain a complete transcript including a start and stop codon and any other annotated features.

The finalize () method affords any annotation format the benefit of not annotating redundant features, such as introns, which are implied by the flanking coding sequences.

CONSTANTS

Blacklist Values
    These functions explain a reason why a transcript was thrown away, if it was. The value of the blacklisted member variable is set to one of these if nonzero.

    OVERLAP
        The transcript has an overlap.

    OUTOFBOUNDS
        The transcript is out of the bounds of the underlying sequence (begin is < 0 or end > length of sequence).

    NEGLENGTH
        A feature was created with a greater or equal start coordinate than end coordinate.

    AMBIGUOUS
        There was a point in the transcript where in finalizing an unfilled feature between two states had more than one potential states.

    NOGAP
        There was a gap between two states for which there was no valid state in the defined HMM to fill it with.

    NOFEATURES
        There were no features in the transcript when it was brought to finalize.

    BADTRANS
        There was a bad transition between two features which butted up against each other.

FUNCTIONS

new ([transID, [geneID]])
    Create a new empty transcript. Add features to the transcript with the add (), or via a FeatureMapping. You may pass a transcript ID to identify it and optionally, you may pass a geneID. If no ID is passed, one will be assigned.

clone
    Create a copy of an object instance.

id ()
    Return the transcript ID. This will only return something if the transcript has been finalized.

geneID ()
    Return the gene ID of the transcript. This may or may not be defined depending on the AnnotationPlugin.

features ()
    Return an array reference to the features in the transcript. These are of type iPE::Annotation::Feature.

min ()
    Return the 5' most coordinate of the transcript for all annotated features.

max ()
    Return the 3' most coordinate of the transcript for all annotated features.

finalized ()
    Return 1 if the transcript has been finalized, 0 otherwise. A finalized transcript is a transcript whose has all positions covered from the min to max coordinate, and whose features are all sorted in order of position.

blacklisted ()
    If the transcript has become useless because it has an odd feature, it becomes blacklisted. All blacklisted transcripts should be ignored. The value of the blacklist is the reason for blacklisting.

addFeature (state, start, end[, startFrame[, endFrame]])
    Add a feature to the transcript. The state is expected to be an iPE::State object. The start and end coordinates are a 0-based index and cannot overlap. The script dies if the feature overlaps with another in the transcript.

    If a start frame or end frame is not suppled, it is assumed to be 0.

    These can be added automatically with the iPE::FeatureMapping object.

    Returns the newly created feature.

removeFeature(feature)
    Remove a feature from a Transcript. Pass a reference to the feature you wish to remove.

finalize (length[, transID[, geneID]])
    Finalize the transcript by filling in the gaps. length is the length of the underlying sequence. It is used to check that the transcript does not overstep the bounds of the sequence.

setLevels (levels)
    Set the level of all the features of a transcript according to the iPE::GCContent object passed in.

SEE ALSO
iPE::Feature, iPE::FeatureMap, iPE::Annotation, iPE

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu).

POD ERRORS
Hey! The above document had some coding errors, which are explained below:

Around line 429:
    You forgot a '=back' before '=head1'