Rewriting PROKKA_COG to be more flexible and readable
Unfinished changes
Merge pull request #63 from BinPro/develop

Version 0.2.2 released.
Merge branch 'master' into prodigal_cog
Replaced the PROKKA_COG.py and Validate_scg.pl script with COG_table.py
Tests for COG_table.py script
COGPlot script accepts full output from COG_table.py, without need for cut step
Need bcbio-gff for travis to run tests for COG_table.py
Extended colourscale for cogplot to work for larger number of cogs
Added an optional parameter for separating the contig id and the protein id if no gff file is used
Started filling in how to use the new COG_table.py script.
Updated documentation for new COG_table.py script.
Spellfix
Changed name of script within comments
Moved marker gene file
Removed duplicated scg file
Changed reference to scgs accordingly
Merge pull request #64 from alneberg/prodigal_cog

Collapse PROKKA_COG and Validate_scg.pl scripts into one.