noncoding genes from imported Prokka

[Emily St. John]

Hi Anvi'o team, 

I've had an occasional issue when building contigs databases from external gene calls that I generated in Prokka, and imported using gff_parser.py.  In the external-gene-calls.txt file, all my genes are marked as call type 1 and non-partial. However, when I generate the contigs database, a couple of the genes are flagged as noncoding and are excluded from the database. Any ideas why this may be happening? 

Thanks so much for your help, and for developing this fantastic suite of tools.

~Emily St. John

[A. Murat Eren (Meren)]

Hello there,

Did you try to turn off this functionality by providing this flag to anvi-gen-contigs-database (sorry for the typo in the first sentence of the help -- I just realized it)?

  --skip-predict-frame  When you have provide an external gene calls file,

                        anvi'o will predict the correct frame for gene calls

                        as best as it can by using a previously-generated

                        Markov model that is trained using the uniprot50

                        database (see this for details

                        https://github.com/merenlab/anvio/pull/1428), UNLESS

                        there is an `aa_sequence` entry for a given gene call

                        in the external gene calls file. Please note that

                        PREDICTING FRAMES MAY CHANGE START/STOP POSITIONS OF

                        YOUR GENE CALLS SLIGHTLY, if those that are in the

                        external gene calls file are not describing proper

                        gene calls according to the model. If you use this

                        flag, anvi'o will not rely on any model and will

                        attempt to translate your DNA sequences by solely

                        relying upon start/stop positions in the file, but it

                        will complain about sequences start/stop positions of

                        which are not divisible by 3. (default: False)

Best wishes,

--

A. Murat Eren (Meren) | he/him

https://merenlab.org | https://anvio.org | @merenbey

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Emily St. John]

Hi Meren, 

That worked perfectly. Thanks!

~Emily