#53 Proteins2CDS.pl

[Arnaud Kerhornou]

The script doesn't work on multiple-entry fasta (DNA)
input files. THe reason is because exonerate
protein2genome model has a bug. Guy Slater
(guy@ebi.ac.uk) is aware of the bug (I think, or maybe
he has forgotten about it!!) but hasn't fixed it yet.

This bug is that exonerate reports reverse strand
features coordinates AS ATTACHED to the complement
sequence NOT the forward sequence !!!

I have made a patch in the PSU ExonerateGFF.pm parser
module to fix it temporaly. When Guy has fixed it, the
patch can be removed in our Exonerate parser. Then the
script should then be able to cope with mutiple-entry
fasta file.

(e.g. you could then give a set of chromosomes).