Hello, I am trying to use biopython to run the local blast. I created the database for Ecoli strain MG6155 and the output results were in nsq format. Now I want to run the local blast using biopython. I am doing:
result_handlel= NcbiblastnCommandline(query="l70.fasta", db = "MG1655.nsq", out = 'resultl.xml', outfmt= 5)
os.system(str(result_handlel))
However python will not read the nsq file. I tried to look at biopython documentation and couldn't find a way to read the file. Any knows how to read and pass in an nsq data base in NCBIblastnCommandLine?
Thanks