search

KennthShang / PhaGCN2.0

27 stars 10 forks source link

Why diamond in run_Speed_up.py？ #13

Closed Asa12138 closed 3 days ago

Asa12138 commented 3 weeks ago

Hello, I found that run_Speed_up.py has to run diamond and blastp every time, but in fact this part is just database preparation, which should be enough once. Why should it be run in run_Speed_up.py every time? It takes at least dozens of minutes each time, and the obtained database.dmnd and other files will be overwritten next time.

Asa12138 commented 3 weeks ago

I also found that the diamond library was built for ALL_protein.fasta in run_KnowledgeGraph.py. If several tasks are run at the same time, there will definitely still be problems. The principle of running the program without changing the database itself and only generating intermediate files and output files should be followed for optimization. Looking forward to PhaGCN doing better.

yuanwenguang666 commented 2 weeks ago

Dear! Thank you for your valuable suggestion. I'm sorry we didn't notice that before. The corresponding function will be added in the next week's update. Thank you again for your suggestions about PhaGCN2 , It's useful. All the best!!! Wen-Guang

yuanwenguang666 commented 3 days ago

Thank you for your advice. It has been fixed in the updated version.