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qiyunlab / HGTector

HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
BSD 3-Clause "New" or "Revised" License
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about datase build #117

Closed manik-123 closed 1 year ago

manik-123 commented 1 year ago

when i run hgtector database -o db_dir --default I get the below error

Done. Total number of genomes in categories: 288353. Filtering genomes... Traceback (most recent call last): File "/project/liuguohong/anaconda3/envs/hgtector/bin/hgtector", line 96, in main() File "/project/liuguohong/anaconda3/envs/hgtector/bin/hgtector", line 35, in main module(args) File "/project/liuguohong/anaconda3/envs/hgtector/lib/python3.8/site-packages/hgtector/database.py", line 134, in call self.filter_genomes() File "/project/liuguohong/anaconda3/envs/hgtector/lib/python3.8/site-packages/hgtector/database.py", line 394, in filter_genomes self.df['accnov'] = self.df['accession'].str.split('.', 1).str[0] File "/project/liuguohong/anaconda3/envs/hgtector/lib/python3.8/site-packages/pandas/core/strings/accessor.py", line 129, in wrapper return func(self, *args, **kwargs) TypeError: split() takes from 1 to 2 positional arguments but 3 were given

manik-123 commented 1 year ago

I solved it

zouminghong commented 1 year ago

I solved it

Hello，I‘m encountering the same problem. How do you solve it？ Looking forward your replay.

manik-123 commented 1 year ago

I solved it

Hello，I‘m encountering the same problem. How do you solve it？ Looking forward your replay. You may have to completely delete the conda environment and create it again. please use this...... conda create -n hgtector -c bioconda python=3.7.7 pyyaml=5.3.1 pandas=1.0.3 matplotlib=3.1.3 scikit-learn=0.22.1 diamond blast=2.9.0

qiyunzhu commented 1 year ago

Hello @manik-123 @zouminghong Thanks for reporting this bug. Sorry that I didn't get to it until now. Well I just fixed it (#118 ). It was a compatibility issue with newer versions of Pandas. You can update HGTector with:

pip install --force-reinstall --no-cache-dir git+https://github.com/qiyunlab/HGTector.git

Then the problem should be solved. Please let me know if that works for you. Thanks!

manik-123 commented 1 year ago

Thank you so much

qiyunzhu commented 1 year ago

@manik-123 Just fixed another bug #119 You need to update again if you did so in the past few minutes :)

manik-123 commented 1 year ago

Okay, I will update it again

manik-123 commented 1 year ago

Thank you for the update