Based on the main branch environment, what will happen to the res.phylo.to_fasta_ dev (os. path. join (out_cath, "db", names [i * search_datch+j]+'. fasta') method of phylopandas

ml4bio / Dense-Homolog-Retrieval

Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval

BSD 3-Clause "New" or "Revised" License

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Based on the main branch environment, what will happen to the res.phylo.to_fasta_ dev (os. path. join (out_cath, "db", names [i * search_datch+j]+'. fasta') method of phylopandas #9

Closed ArtBioDesign closed 2 months ago

ArtBioDesign commented 2 months ago

Based on the main branch environment, what will happen to the res.phylo.tofasta dev (os. path. join (out_cath, "db", names [i * search_datch+j]+'. fasta') method of phylopandas File "/hpcfs/fhome/xxxx/.conda/envs/dprv3/lib/python3.9/site-packages/phylopandas/seqio/write.py", line 183, in _write
seq_records.to_csv(filename, sep='\n', header=False, index=False, line_terminator='\n>', mode='a+') TypeError: to_csv() got an unexpected keyword argument 'line_terminator'

heathcliff233 commented 2 months ago

Thank you for the report. Currently I have removed the dependency on phylopandas due to numerous compatibility issue and supports tsv format input. Please try to pull again. The problem you see here is probably due to different args in different pandas version.