Include an optional ORF prediction step

[iimog]

Having an optional ORF prediction step (using established software like getorf from EMBOSS) would allow using assembled nucleotide sequences as input. Therefore the requirement to annotate genomes first could be dropped. It is also possible to auto-detect if fasta files contain aa or nt sequences. So even mixed input without explicit specification would be possible.

[jdguzmanv]

Would be really great to have bcgTree 2.0 working also on nucleotide level. Input could be an annotated Genbank file, or a nucleotide genome fasta file and bcgTree calling an a fifth tool such as Prokka or Prodigal for annotation.

[iimog]

Thanks for the feedback. I agree that this would be a very useful feature. I'll have another look at it to see if it can be quickly implemented. I'll keep you posted.

[iimog]

Hey @jdguzmanv I implemented an optional translation step. You can now provide fasta files either via --proteome as peptide fasta files or via --genome as nucleotide fasta files. Each fasta file that you provide as --genome is first translated with prodigal (which needs to be installed and available). I also added the new options to the GUI.

It is not merged into the master branch yet, so please have a look in the feat-nuc2pep branch: https://github.com/molbiodiv/bcgTree/tree/feat-nuc2pep
Let me know what you think. I'll work on polishing and merging this feature next week.

[iimog]

This feature is part of the latest release (v1.2.0 released a couple of minutes ago). Please try it and let me know if you have questions or suggestions for improvement.