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.

[TreeT2]

Hi All,

Is this available in v1.12 or will we have to wait till v1.13?

Thanks