Display COG annotations on circle phylogram

[e1pi...@ucsd.edu]

Hi! 

Has anyone come up with an elegant solution to somehow display COG annotations on the circle display?  I was thinking of something like doing a stacked bar for each split with the bars showing the relative percentage of each COG category (mobilome, defense mechanisms, etc.).  Just wondered if there are any easy ways to display the functional information on the whole diagram...

Best, 

Emily 

[A. Murat Eren]

Hi Emily,

Please take a look at anvi-search-functions-in-splits program. Here is an example use:

anvi-search-functions-in-splits -c CONTIGS.db

                                --search Glycosyltransferase,Uracil,MOREFUNCTIONS

                                --verbose

                                --full-report full-report.txt

                                -o hits.txt

You can add the resulting file `function-hits.txt` to `anvi-interactive` using the parameter `--additional-layers` to display in which contigs those functions are found.

I hope this helps.

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: twitter :: gpg

--
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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[Varun Srinivasan]

HI Meren,

I was wondering if there was a way to get the split information for external gene calls that the user had imported. I am trying to display a few external annotations that I imported from Prokka using custom HMMs and would like to get split information for them specifically without having to specify every function. If not, getting information for all of them would also be helpful so that I can use a script to filter the gene calls that I need. 

On a related note, I modified the gff_parser.py script to output HMM/inference source to gene-annot.txt file. So the information is in the contigs db. It would be useful if the user can use this information to filter! 

Thanks

Varun

P.S. if this capability doesn't exist and you think it would be useful, I can add it as an issue in github!

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[A. Murat Eren]

Hi Varun,

Please try the program anvi-export-gene-calls and take a look at the output :)

Yes, we could improve our filters for search operations. Ozcan and I are thinking about a major redesign of the codebase, after which it will be trivial to add these kind of features. Please feel free to submit an issue.

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: twitter :: gpg

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[Varun Srinivasan]

Thanks Meren! Should have seen that function!