Phanotate

Fixed
- An error in the fastpath package that caused the best path not to be found if edges had large enough weights. This is because of rounding errors for long doubles, and that C cannot distinguish between 1E50 and 1E50 + 1
Changed
- Switched from using fastpath to fastpathz, which uses infinite-precision integers

Fixed
- An error in the fastpath package caused by not emptying out the graph between contigs, if the input file has more than one contig

Added
- Missing MANIFEST.in file

Changed
- All changes in this version are merely optimization and organization, output should be identical to previous versions.
- Reorganized phanotate into a package that installs via setup.py script or through pip
- Coded up fastpath into a Cython pypi extension that is fetched and installed via pip
- Renamed the modules folder

Fixed
- An error that was caused by newer versions of tRNAscanSE using the -b flag to indicate a bed file, instead of the earlier versions where this flag was to output brief format. Using the long arg --brief is compatible with all versions.
- An error where the ouput from tRNAscanSE with popen was not decoded from bytes to string properly.

Fixed
- An error that was caused by connecting the wrong types of CDS and tRNA in the graph network

Added
- Displaying the weights (scores) of ORFs in the genbank out file format