Entering edit mode
8.2 years ago
djd17
•
0
Hi I am new to working with blast on a local database. I am using biopython in a canopy shell I would like to be able to blast all the sequences within a fasta file using NcbiblastnCommandline
. currently it only gives results for the first sequence in the file. I have searched high and low for a solution it really should not be complicated
from Bio.Blast.Applications import NcbiblastnCommandline
blastn_cline = NcbiblastnCommandline(query="SLQuery.fasta", db="S1.db", evalue=0.001, outfmt=5, out="SLQuery_vs_S1.xml")
blastn_cline()
I have tried opening the fasta in read format and then blasting no luck
any help is appreciated..I am new to programming so very clear instructions would be preferred :) Thanks