So I'm writing a script to run a blast query, which I hardcoded variables for at this point (just to make sure they weren't getting messed up). Which is:
blastCLine = NcbiblastnCommandline(query="temp.fasta", db="refseq_rna", outfmt=5, out="test.txt", evalue=0.05) stdt, stdr = blastCLine() print stdt print stdr
And I get nothing, output file is blank, and no error or anything. If I use the blast command from blastCLine on the command line, it works. If i use the above code in the python environment, it works. Just not working in my script.
I've been googling and looking at tons of examples. From what I can tell it should work. I've tried changing it to blastx, and using cmd="blastn" to no avail, also. Any suggestions?