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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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making plant database with error #116

Closed zouminghong closed 1 year ago

zouminghong commented 1 year ago

Hello,Qiyun！Thank you in advance for developing such an amazing tool. I meet an error when I create the plant database and I'm a little confused about it.

(hgtector) [zou@localhost ~]$ hgtector database -o db_dir --cats plant --sample 5 --threads 32

Database building started at 2023-05-05 03:04:58.094068. Using local file taxdump.tar.gz. Reading NCBI taxonomy database... done. Total number of TaxIDs: 2502076. Downloading RefSeq assembly summary... done. Reading RefSeq assembly summary... done. Total number of genomes: 301820. Genome categories: plant Downloading genome list per RefSeq category... plant: 160 Done. Total number of genomes in categories: 160. Filtering genomes... Traceback (most recent call last): File "/home/zou/anaconda3/envs/hgtector/bin/hgtector", line 96, in main() File "/home/zou/anaconda3/envs/hgtector/bin/hgtector", line 35, in main module(args) File "/home/zou/anaconda3/envs/hgtector/lib/python3.10/site-packages/hgtector/database.py", line 134, in call self.filter_genomes() File "/home/zou/anaconda3/envs/hgtector/lib/python3.10/site-packages/hgtector/database.py", line 394, in filter_genomes self.df['accnov'] = self.df['accession'].str.split('.', 1).str[0] File "/home/zou/anaconda3/envs/hgtector/lib/python3.10/site-packages/pandas/core/strings/accessor.py", line 129, in wrapper return func(self, *args, **kwargs) TypeError: StringMethods.split() takes from 1 to 2 positional arguments but 3 were given

Could you please help me with this issue? Looking forward your replay.

qiyunzhu commented 1 year ago

Fixed in #118