Pyparanoid

Upgraded entire package to python3
Fixed several issues with genbank downloading errors and inability to parse
gene annotations for non-Ensembl genomes (i.e. RefSeq, IMG and Prokka)

Tested successfully on MacOSX and on a UNIX cluster.

Version for UBC bootcamp, minor changes.

-fixed methods for getting genomes from Ensembl
-added a way to incorporate IMG genomes to genome metadata
-added plot_multigene_presence() to genomeplot
-added select_rep_strains() to genomeplot

The biggest change is that the homolog and prop_homolog fasta files are now stored as a single file, rather than a folder containing 10s of thousands of individual fasta files.

Fixed bug where hmm files were empty due to incorrect function call in BuildGroups.py

First official release!

Pipeline should work reasonably well if you install with pip and have dependencies installed.
Consult README.md and analysis_ipython notebooks for help.