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It is much faster after replacing usearch with vsearch with multi threads. Thanks for your suggestions @tseemann. The modification can be done for the usearch_multi.py from line 26 to 39.
Here is the updated code:
#run usearch
args = []
args.append(USEARCH_PATH)
args.append('--usearch_global')
args.append(path + sp + '/genes/' + prot1)
args.append('--db')
args.append(path + sp + '/genes/' + prot2)
args.append('--id')
args.append('0.7')
args.append('--threads')
args.append('32') ## This can be changed based on your dataset
args.append('--strand')
args.append('plus')
args.append('--blast6out')
usearch is not open source
can you replace it with vsearch?
https://github.com/torognes/vsearch
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