Adding support for partial genes

[lguy]

Shortly:

• prodigal can now be run without the -c option
• prodigal's gff output is now parsed with Bio::Tools:GFF, using the 'partial' tag of prodigal to find gene running off edges.
• Bio::Location::Fuzzy is used to correctly set start and end of CDSs. I also set the frame and codon_start attributes.
• Some tweaking is performed to correctly print the tbl file, but I think I covered all possible cases.
• Added a new --partialgenes option to prokka

[tseemann]

@lguy Lionel I am sorry this pull request has been ignored. I think I was overwhelmed by it, as I don't have proper test suite, and also I had a major job change at the end of last year. You deserved a better response from me! Do you think you could tweak it to merge cleanly with HEAD? How do you feel we should proceed?

[lguy]

@tseemann Torsten, thanks for coming back with that. I feel the changes I made need to be carefully examined and run through more test sets than I have before they are merged. I'm currently unable to spend much time on this, but I can give a shot in the coming week, see if I can go through the conflicts and run some more tests. I've also gone through a major job (and computer) change and I need to reinstall many things before I'm up and running again...

[jcmcnch]

@lguy @tseemann Hi Lionel and Torsten, I'm very interested in this addition to prokka for an analysis of single-cell genomic data where I have many short contigs with genes running off the edges. Given the popularity of single-cell genomics for environmental microbiologist types, I'm sure there would be quite a bit of interest from others as well. Is there anything I can do to help make this into a reality? I have a dataset that I could test the changes on and could check for potential bugs if that would be useful to you. Let me know if you think I can offer any help here. Cheers, Jesse

[lguy]

@tseemann @jcmcnch Jesse,
Two students (Joran Martijn - @novigit and Jennah Dharamshi - @jennahd) at Thijs Ettema's lab have been working to merge the pull request into a recent HEAD. AFAIK they are done and were testing it a bit further before filing a pull request. I'll ask them, but I'm confident they'd be happy to use your help to test the updated code.

[jennahd]

Hi @tseemann @jcmcnch @lguy,

@novigit and I have added the changes made by Lionel to the prokka version 1.12 and have also fixed an issue with frameshifts during translation of some partial genes (pull request #219). We also ran a few tests. @jcmcnch, it would be great if you could test our changes with your dataset (Let us know if there is anything we can do to help)!