Hello, I am a Computer Science & Molecular Biology Student at MIT. I am currently working on my research project in the Research Laboratory of Electronics and I am trying to solve a problem while using Blast locally but I have been running in to problems doing so even though I am doing exactly what the documentation needs me to do. I was wondering if there is anyone used blast locally before? There's no one in my lab who can help me with it so was wondering if there's anyone who can help me with this?
Basically to get a blast output I am using the command line:
result_handler = NcbiblastnCommandline(query= "r70.fasta", db = "MG1655.fasta", out = 'resultr.xml')
os.system(str(result_handler))
But it does not output anything in the resultr.xml file # MG1655.fasta is the data base that I want to search against. I tried the doing the MG1655.txt version too and it still did not work.
Thanks,
