Hello everyone, I am new to 'real' bioinformatics and have been trying to call blastn with the biopython NcbiblastnCommandline() function on a local fasta database. It does not return an error and fails to output a xml file. My blast programs work and are in the path. I can blast against the database from the terminal and I am able to access the web based NCBI blast using biopython. My os is OS X 10.8.3.
import os from Bio import SeqIO from Bio.Blast.Applications import NcbiblastnCommandline as blastn seqs = [seq_record for seq_record in SeqIO.parse('spiking.fasta','fasta')] os.chdir('/Users/christopherrichardrivera/Desktop/blastdb') blast = blastn(query=TheSeq, db='repSetBlast', outfmt=5, out='blastresult.xml')
There is no output to screen, printing blast returns:
blastn -out sequence1.xml -outfmt 5 -query ID: AB
Number of features: 0
Seq('CCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGGGGAACCCTGATCCAG...AAT', SingleLetterAlphabet()) -db repSet -evalue 0.01
Thank you very much.