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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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anvi-display-functions doesn't recognize --gene-caller flag #1847

Closed VManning closed 2 years ago

VManning commented 3 years ago

Short description of the problem

anvi-display-functions doesn't recognize --gene-caller flag

anvi'o version

hope (v7.1)



## System info

MacOs Big Sur on a Mac Pro with 3.2 GHz 16-Core Intel Xeon W Processor, 96 GB 2933 MHz DDR4 Memory. Anvi'o was installed with miniconda

## Detailed description of the issue

I intended to use anvi-display-functions to display COG annotations for diverse genomes of a low complexity metagenome to get an idea of enriched functions in the different genomes. These genomes had been annotated with RastTk in another platform. The external-gene-calls file contains Kbase-Rasttk in the source column.

Ran this command:
anvi-display-functions -e external_genomes.txt -g pan1-5-GENOMES.db --annotation-source COG20_FUNCTION -p COG20-PROFILE.db --min-occurrence 2

Config Error: None of your genomes seem to have a gene call, which is a typical error you get
       if you are working with contigs databases with external gene calls. You can   
       solve it by looking at the output of the program `anvi-db-info` for a given   
       contigs database in your collection, and use one of the gene caller sources   
       listed in the output using the `--gene-caller` parameter. 

Reran with --gene-caller flag
anvi-display-functions -e external_genomes.txt -g pan1-5-GENOMES.db --annotation-source COG20_FUNCTION -p COG20-PROFILE.db --gene-caller Kbase-Rasttk --min-occurrence 2  

And got this:
anvi-display-functions: error: unrecognized arguments: --gene-caller Kbase-Rasttk 

There appears to be a bug.
meren commented 2 years ago

This should be now done. Thank you very much for the report, @VManning!

VManning commented 2 years ago

Hi @meren,

Thank you for working on this. Unfortunately I tried again and got the same error:

(anvio-7.1) manniv@x86_64-apple-darwin13 PAN12 % anvi-display-functions -e external_genomes.txt -g pan12-GENOMES.db --annotation-source COG20_FUNCTION --gene-caller Prodigal -p COG20-PROFILE.db --min-occurrence 2

usage: anvi-display-functions [-h] [-i FILE_PATH] [-e FILE_PATH]
[-g GENOMES_STORAGE] [-G TEXT_FILE] [--print-genome-names-and-quit] --annotation-source SOURCE NAME [--aggregate-based-on-accession] [--aggregate-using-all-hits] [--min-occurrence NUM GENOMES] -p PROFILE_DB [--title NAME] [--state-autoload NAME] [--collection-autoload NAME] [--export-svg FILE_PATH] [--dry-run] [--skip-news] [-I IP_ADDR] [-P INT] [--browser-path PATH] [--read-only] [--server-only] [--password-protected] [--user-server-shutdown] [--version] [--debug] [--force] [--fix-sad-tables] [--quiet] [--no-progress] [--as-markdown] [--tmp-dir TMP_DIR] [--display-db-calls] [--force-use-my-tree] anvi-display-functions: error: unrecognized arguments: --gene-caller Prodigal

Shucks!

ivagljiva commented 2 years ago

Hi @VManning, the bug fix that Meren did was pushed into our development branch, so you will not see it reflected in v7.1 :)

You should install the dev branch by following the instructions here and then try again with that version of anvi'o!

VManning commented 2 years ago

Oh, That makes a lot of sense.

Sounds scary, but I’ll try it (I am not a wizard!)

v

From: Iva Veseli @.> Date: Wednesday, December 15, 2021 at 9:49 AM To: merenlab/anvio @.> Cc: Manning, Viola @.>, Mention @.> Subject: Re: [merenlab/anvio] anvi-display-functions doesn't recognize --gene-caller flag (Issue #1847)

Hi @VManninghttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FVManning&data=04%7C01%7C%7C7c324e0b541642e9e8a608d9bff33143%7Ced5b36e701ee4ebc867ee03cfa0d4697%7C0%7C0%7C637751873489301268%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=mfIv1iBoeZLzU0cXOsr%2FAPUbViZMyi%2BYrpcC9G14ogk%3D&reserved=0, the bug fix that Meren did was pushed into our development branch, so you will not see it reflected in v7.1 :)

You should install the dev branch by following the instructions herehttps://gcc02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmerenlab.org%2F2016%2F06%2F26%2Finstallation-v2%2F%235-follow-the-active-development-youre-a-wizard-arry&data=04%7C01%7C%7C7c324e0b541642e9e8a608d9bff33143%7Ced5b36e701ee4ebc867ee03cfa0d4697%7C0%7C0%7C637751873489301268%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=YXzl1q8g5nfeQJVGmFjnnmM14%2By9MIfGoN%2Ff078lr2o%3D&reserved=0 and then try again with that version of anvi'o!

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ivagljiva commented 2 years ago

Anyone can be a wizard! 😉

Feel free to let us know if you run into issues!