blast all sequences within a fasta file
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
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Can you please post the output of
head SLQuery.fasta?sorry what do you need? I don't understand....total nube here. i have a few of these files i have created they are fasta format with between 5 and 40 NT sequences i sliced from a contig each sequence is about 40 NT long. all i want is for each sequence to be read and blasted against the database. it currently only reads the first sequence why i have no idea
Can you show us how you fasta looks like ? first few lines ( or seq names) of your fasta file.
Sorry what do you need? I don't understand....
If you are on a Mac or Linux box, type
head SLQuery.fastaso we can see what your FASTA file looks like. Or you can just view the FASTA file in a text editor and paste the first few lines here.Sorry thats what i thought you where asking for. It all seems to be correct form to me. Do I need to parse the file before blasting maybe?
Try taking out that blank line between the first and second lines and see if it does the first two sequences instead of only the first one. If that works then the empty line is probably the reason for your problem.