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yuzhiguo07 / EPTool

A New Enhancing PSSM Tool for Protein Secondary Structure Prediction
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Cannot find run_hmmer.py #1

Open ndnng opened 2 years ago

ndnng commented 2 years ago

Hi, the repo seems not having run_hmmer.py

yuzhiguo07 commented 2 years ago

Sorry for the inconvenient. I finished this part of the work during the internship with my co-workers, due to copyright reasons we can not provide this part of the script. But I can provide the arguments to Jackhmmer, and you can write your own simple script and fit the output file to the aln_example/sample.aln format. Here is the jackhmmer running command: 

phmmer -E 1 --domE 1 --incE 0.01 --incdomE 0.03 --mx BLOSUM62 --pextend 0.4 --popen 0.02 -o {out_path} -A {sto_path} --notextw --cpu {cpu_num} {fasta_path} {db_path}