[Bioperl-l] Bio::Tools::Glimmer

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Mon Oct 18 10:50:42 EDT 2004


I am a bit confused about the state of the Bio::Tools::Glimmer module.
I have glimmer version 2.13 and Bioperl-1.4.  The glimmer website
(http://www.tigr.org/software/glimmer/) states that version 2.13 is the
current release.

In Bio::Tools::Glimmer, in sub _parse_predictions, not only is there a
comment which confidently states "# glimmer 3.0 output", it tests for a
line which says "Predicted genes" whereas glimmer 2.13 outputs "Putative
Genes".  On testing the module with glimmer 2.13 output, the module is
not successful, presumably as it is based on version 3.0 output.

Is there a reason the bioperl module is based on glimmer 3.0?


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