May 26, 2018

Handler for FeatureIO

BioFeatureIO is an iterator subsystem for genomic sequence features.

BioFeatureIO is a handler module for the formats in the FeatureIO set eg, BioFeatureIOGFF. It is the officially sanctioned way of getting at the format objects, which most people should use.

The BioFeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules eg, GFF format, or BED format and can either read or write feature objects BioSeqFeature objects, or more correctly, BioFeatureHolderI implementing objects, of which BioSeqFeature is one such object. If you want to know what to do with a BioSeqFeatureI object, read BioSeqFeatureI.

The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the BioFeatureIOgff object.

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