Merck / Merck/deepbgc

using deepBGC with metagenomes

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Description

Dear users, I wonder if I can use deepBGC with metagenomic samples? In the paper describing the software it is mentioned as a useful tool for this kind of data but I don't know if it is implemented in the current version. I run a test with a sample (CPB-18) which is the scaffold file obtained from SPAdes and it quickly returned 0 matches I don't understand if this is a matter of the format I used or something else. This same file returned several matches or bgc with antiSMASH.

I noticed these lines while running it

/mnt/ubi/andres/miniconda3/envs/deepbio/lib/python3.7/site-packages/sklearn/utils/deprecation.py:143: FutureWarning: The sklearn.tree.tree module is deprecated in version 0.22 and will be removed in version 0.24. The corresponding classes / functions should instead be imported from sklearn.tree. Anything that cannot be imported from sklearn.tree is now part of the private API. warnings.warn(message, FutureWarning) /mnt/ubi/andres/miniconda3/envs/deepbio/lib/python3.7/site-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator DecisionTreeClassifier from version 0.18.2 when using version 0.23.2. This might lead to breaking code or invalid results. Use at your own risk. UserWarning) /mnt/ubi/andres/miniconda3/envs/deepbio/lib/python3.7/site-packages/sklearn/base.py:334: UserWarning: Trying to unpickle estimator RandomForestClassifier from version 0.18.2 when using version 0.23.2. This might lead to breaking code or invalid results. Use at your own risk.

Before that I run the BGC sample included within the test folder and I obtained 2 hits as seen in the log attached here (BGC15 file).

Maybe I have a broken install of the program, I followed the conda instructions.
Please find attached the log from deepbgc info too.
pipeinfo.txt

BGC15.txt
sample.txt

Thanks for your help.

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  3. Fork the repository and make your change on a branch.
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Research direction

Start by reviewing the attached pipeinfo.txt, BGC15.txt, and sample.txt logs, then compare the CPB-18 scaffold input with the BGC sample in the test folder. Determine whether metagenomic scaffold files are supported and whether the zero matches stem from input format, installation, or the reported scikit-learn warnings; document the finding and expected behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, scikit-learn
Domain
bioinformatics, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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