Started adding more documentation about how to use proc_phytozome.pl script
Added new section of code that processes the annotation file for each species in Phytozome.
From this file it extracts the 'local' transcript ID (i.e. that used by the source database)
and includes this in the final output in a new column.

It also extract the best A. thaliana ortholog information from the same file and includes this
in the final output (adding NA if no ortholog listed by Phytozome). For A. thaliana, this information
gets extracted as the best rice ortholog. Still need to check what happens in other species.