I'm using the standalone BLAST 2.2.17 with python. However, I'm having a problem with the cmd. When running the script the cmd stops responding at the 15th blast record. It doesn't matter if I change the proteins, it's always the 15th.
from Bio.Blast import NCBIStandalone
from Bio.Blast import NCBIXML
my_blast_db = r"C:\Niek\Test2.2.17\Worm\c_elegans.protein.WS200.fasta"
my_blast_file = r"C:\Niek\Test2.2.17\Worm\worm-HD.fasta"
my_blast_exe = r"C:\Niek\blast-2.2.17\bin\blastall.exe"
result_handle, error_handle = NCBIStandalone.blastall(my_blast_exe, "blastp",
my_blast_db, my_blast_file, matrix="BLOSUM62")
blast_records = NCBIXML.parse(result_handle)
y = 0
#see if target is in TF list
for blast_record in blast_records:
if blast_record:
y+=1
print y
It worked normally like this earlier today and with other databases.
Has anyone else had this problem/know how to fix it?
Thanks,
Niek
Edit: I used blast 2.2.17 in command line directly (using same commands as used above) to create an xml file and read that in as result_handle. That works.
@Michael's comment:
from Bio.Blast.Applications import NcbiblastpCommandline
my_blast_db = r"C:\Niek\Test2.2.17\Worm\c_elegans.protein.WS200.fasta"
my_blast_file = r"C:\Niek\Test2.2.17\Worm\worm-HD.fasta"
blastp_cline = NcbiblastpCommandline(cmd='blastp', query=my_blast_file, db=my_blast_db, evalue=0.01,
outfmt=5, out ...