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BrendelGroup / AEGeAn

Integrated toolkit for analysis and evaluation of annotated genomes
http://brendelgroup.github.io/AEGeAn
ISC License
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Orientation attribute for iiLoci #143

Closed standage closed 9 years ago

standage commented 9 years ago

It would be helpful to include an orientation attribute for intergenic iLoci, showing the orientation of the flanking piLoci/niLoci. There would be 4 possible values.

>>     Both genes forward
<<     Both genes reverse
><     Genes oriented toward each other
<>     Genes oriented away from each other

This would be handled pre-refinement, since that is the only stage at which (positive-length) iiLoci are dealt with. If the right flank contains overlapping genes/piLoci, orientation is determined by the first gene (easy to retrieve since they are stored in sorted order). If the left flank contains overlapping genes/piLoci, orientation is determined by the gene with the right-most end coordinate (not necessarily the last gene).

standage commented 9 years ago

Decided to use the following instead (for encodings' sake).

FF     Both genes forward
RR     Both genes reverse
FR     Genes oriented toward each other
RF     Genes oriented away from each other