I have been using Biopython to make scripts to run sequences through BLAST. I'm using the command:
Here is the beginning of most of my scripts:
import sys, os from Bio import SeqIO, Entrez, SearchIO from Bio.Blast import NCBIWWW, NCBIXML from ftplib import FTP from urllib.error import HTTPError fasta_string = open(sys.argv).read() result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string, hitlist_size=10) save_file = open("my_blast.xml", "w") save_file.write(result_handle.read()) save_file.close() result_handle.close()
I couple months ago I had no problem running these scripts, now none of them will run but I will receive no error from the script. It will just look like its running but get suck at the above BLAST command. Is anyone else having a similar issue? If so were you able to fix it?? Thanks so much for the help!!