I can't make NcbiblastnCommandline work. Creates the outfile but it's empty.

Question

[madeltutor]

def blast():

from Bio.Blast import NCBIXML
from Bio.Blast.Applications import NcbiblastnCommandline
cline = NcbiblastnCommandline(query="sequence.fasta", db="nt", outfmt=6, out="blast.tbl")
outfile = open("blast.tbl", "w")
outfile.write(cline.parse())
outfile.close()
cline.close()

[Ram]

Please read through this post: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies

You will have to rewrite your question to get a relevant response from the community. When people see that the post text is just code, they will skip it.

Answer 1

[Markus]

After defining your command line, you should just "run" it:

cline = NcbiblastnCommandline(query="sequence.fasta", db="nt", outfmt=6, out="blast.tbl")
cline()

This will generate your file blast.tbl