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
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written
by
muneezapatel •
1 answer
I think you just want to drop .nsq from the db name (the BLAST database is not one file, but spread across 3 ending with sq, in or hr)
By the way, Biopython is not parsing anything when you call NcbiblastnCommandline. Thee sorts of function, called "wrappers", create the commands necessary to run an external application.
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