Closed:blast all sequences within a fasta file
0
0
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

blast sequence • 260 views
ADD COMMENT
This thread is not open. No new answers may be added
Traffic: 2656 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6