http://www.bioperl.org/wiki/GTF
Read and write FeatureLists as GFF/GTF formatted files.
The GFF moniker is applied to a variety of tab-delimited formats
that mock the notion of a standard. This class should parse most files
bearing at least a passing resemblance to any of the formats. You will, however, need
to research the semantics of the files you encounter. Generally,
the format consists of 9 tab-delimited fields:
seqname source featureType start end score strand frame attributes
The 9th field consists of key-value pairs separated by semicolons, the first of which JavaGene interprets
as the group id (as used in GFF1). It is the precise meaning of this 9th field that
varies from week to week. The Feature and FeatureList objects provide various utility methods to
ease the task of accessing and using the attributes. The proper interpretation of any
particular attribute, however, is left to you.