https://github.com/carden24/Bioinformatics_scripts
Tip revision: 020af3000eeca9c2e270be798fe7264ece87f22b authored by Erick Cardenas on 30 September 2018, 20:38:24 UTC
Delete create_multiple_f.sh
Delete create_multiple_f.sh
Tip revision: 020af30
remoteblastp.py
# This scripts will do a blast search against the nr database
# The blast program as well as search parameters
# can be specified inthe lines below
# Usage
# python remoteblastp.py <originalfile.fasta> <output.xml>
# 0 1 2
my_perc_ident = 'none'
my_blast_program = 'blastp'
my_evalue_treshold = 0.00001
my_hitlist_size = 10
import sys
import Bio
from Bio import SeqIO
from Bio.Blast import NCBIWWW
from Bio.Blast import NCBIXML
#input
filein = open(sys.argv[1], "r")
#outputs
myout = sys.argv[2]
fileout = open(myout, 'w')
for seq_record in SeqIO.parse(filein, format="fasta"):
# print seq_record
# print seq_record.format("fasta")
result_handle = NCBIWWW.qblast(my_blast_program, "nr", seq_record.format("fasta"), hitlist_size = my_hitlist_size, expect = my_evalue_treshold, perc_ident = my_perc_ident)
fileout.write(result_handle.read())
filein.close()
fileout.close()