Biopython module deprecation warning

[ayesha-mahfuz]

Hello,

I am having some trouble running gotcha on my custom inputs. I setup gotcha using conda, so I believe that all my dependencies are properly installed. However, whenever I try to run gotcha on any of my custom inputs (unaligned sequences, aligned sequences, or phylogenetic tree file), I get this error below:

BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated
Due to the on going maintenance burden of keeping command line application
wrappers up to date, we have decided to deprecate and eventually remove these
modules.

We instead now recommend building your command line and invoking it directly
with the subprocess module.
warnings.warn(
Run Gotcha Main
bold-cli missing in path

I'm not sure how to proceed since gotcha relies on the Biopython module and it is now deprecated. Any advice on how to design probes for my custom inputs would be appreciated. I've also included my script below for reference:

python3 gotcha.py --marker COI-5P -cf 21.fna -c 1 -o CO1_cluster2_probes

python3 gotcha.py --marker COI-5P -ca 21_MSA.aln -c 1 -o CO1_cluster2_MSA_probes

python3 gotcha.py --marker COI-5P -cn 21_tree.nwk -c 1 -o CO1_cluster2_tree_probes

Thanks in advance for your help!

[Kevinnota]

Hi,

Thank you for your feedback! I have now updated 'gotcha' and hope it should fix the errors you got.

The deprecate module we had already removed in the main script but it was still being loaded, so it gave an error but would still make the script run I think, but it's removed now.

The bold-cli is missing message should only appear if you are not providing custom fasta files, there was a bug in the script and it should be fixed now. Its the tool that downloads sequences from bold. This is not part of the conda environment but an executable script that you have downloaded here https://github.com/CNuge/BOLD-CLI. If this tool is not in your path variables, you need to specify the path with --boldcli_path. But this is only required if you are not supling custom files:)

Hope the script runs smoothly now. Let me know if you encounter more problems:)