Added support for partial genes prokka-1.12

[jennahd]

In Summary:

• Prodigal can now be run without the -c option (closed ends) allowing for partial gene prediction.
• Prodigal's gff output is now parsed with Bio::Tools:GFF, using the 'partial' tag of prodigal to find genes running off edges.
• Bio::Location::Fuzzy is used to correctly set the start and end of CDSs. Also the frame and codon_start attributes were set.
• Some tweaking was performed to correctly print the tbl file, think all possible cases are covered.
• Added a new --partialgenes option to prokka.

We (@novigit and I) applied these changes made by @lguy for prokka version 1.11 (issue #37) to prokka version 1.12.

In addition we made one other fix and completed some tests:

• For partial genes on contig edges, in some cases proteins were being called in the wrong frame, but gene translation for these cases works properly now.
• Running with --partialgenes now gives the same ORF predictions as prodigal without -c (except for ORFs that overlap with tRNAs etc. or those otherwise removed by prokka).
• Running without --partialgenes gives the same ORF predictions as prodigal with -c (except for the ORFs that overlap with tRNAs etc. or those otherwise removed by prokka), re. the same output as prokka 1.12 before these changes.
• No frameshift issues with partial genes were noted when running with several different gcode's.

[lguy]

Apart from the two small things in README.md (line 43, should be as in the original; ll. 478 and following, should be as in the original), I'd recommend accepting those changes. I believe they have been tested thoroughly. We've been using the version with --partialgene (based on prokka 1.11) in the past 2 years without issue.
Did @jcmcnh also had the opportunity to test them?

[jcmcnch]

@jennahd @lguy @novigit This is fantastic, thank you so much! I pulled your changed code and ran it on my dataset and it works like a charm. Without the --partialgenes option enabled, I got 2525 ORFs, and with it I get 4590 ORFs! A lot of those new ones are short contigs that might be meaningless but I was also definitely was missing a lot of edge genes contained in larger contigs. Even for some of the shorter contigs that have edges on both sides, prokka gave functional annotations - information I can keep now thanks to your changes!

So bottom line, it definitely works well and allows me to parse the maximum amount of meaningful data from a fragmented assembly. This will be very handy for both SAGs and metagenomes! Many thanks for sharing your hard work!