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blast_script1.py
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blast_script1.py
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#!/usr/bin/env python
from multiprocessing import Pool
import time
import os
import sys
import argparse
from Bio.Blast.Applications import NcbiblastxCommandline
# Copyright(C) 2014 David Ream
# Released under GPL version 3 licence. http://www.gnu.org/licenses/lgpl.html
# Do not remove this comment
# This exists to make the main function easier to read. It contains code to run the argument parser, and does nothing else.
def parser_code():
parser = argparse.ArgumentParser(description='Run BLAST on a set of searchable database using a query that is specified by the user. Results will be stored by the accession number of the database. Currently this script will only accept protein queries, but I will update to automatically run on all types of genes, as most of the information needed for this behavior exists.')
parser.add_argument("-d", "--database_folder", dest="database_folder", metavar="DIRECTORY", default='./db/',
help="Folder containing all BLAST searchable databases to be used by the program.")
parser.add_argument("-o", "--outfolder", dest="outfolder", metavar="DIRECTORY", default='./blast_result/',
help="Folder where the BLAST results will be stored.")
parser.add_argument("-f", "--filter", dest="filter", metavar="FILE", default="",
help="File restrictiong which accession numbers this script will process. If no file is provided, filtering is not performed.")
parser.add_argument("-n", "--num_proc", dest="num_proc", metavar="INT", default = os.sysconf("SC_NPROCESSORS_CONF"), type=int,
help="Number of processors that you want this script to run on. The default is every CPU that the system has.")
# Fix this option, ultimately it should be a folder, that reads in a operon file with the name of operon(s) with a list of gene names and types.
# The program will then take two files, protein and nucleic acid queries and run them. (This would require that there are two seperate, and complementary
# blast databases within this folder. My desire is that it would be two subfolders, 'protein/' and 'rna/' which house these sets of data.
parser.add_argument("-q", "--query", dest="query", default='./operon_query_files/protein_matches.fa', metavar="FILE",
help="A file that contains the BLAST query for every gene of interest in the dataset.")
parser.add_argument("-e", "--eval", dest="eval", default='1e-6', metavar="FLOAT", type=float,
help="eval for the BLAST search.")
return parser.parse_args()
def check_options(parsed_args):
# section of code that checks the database entry
if os.path.isdir(parsed_args.database_folder):
database_folder = parsed_args.database_folder
else:
print "The folder %s does not exist." % parsed_args.database_folder
sys.exit()
# if the directory that the user specifies does not exist, then the program makes it for them.
if not os.path.isdir(parsed_args.outfolder):
os.makedirs(parsed_args.outfolder)
outfolder = parsed_args.outfolder
# Check the filter file
if parsed_args.filter == '' or os.path.exists(parsed_args.filter):
filter_file = parsed_args.filter
else:
print "The file %s does not exist." % parsed_args.filter
sys.exit()
# section of code that deals determining the number of CPU cores that will be used by the program
if parsed_args.num_proc > os.sysconf("SC_NPROCESSORS_CONF"):
num_proc = os.sysconf("SC_NPROCESSORS_CONF")
elif parsed_args.num_proc < 1:
num_proc = 1
else:
num_proc = int(parsed_args.num_proc)
# Check the query file
if os.path.exists(parsed_args.query):
query_file = parsed_args.query
else:
print "The file %s does not exist." % parsed_args.query
sys.exit()
e_val = parsed_args.eval
return database_folder, outfolder, filter_file, num_proc, query_file, e_val
#this function will return all of the files that are in a directory. os.walk is recursive traversal.
def returnRecursiveDirFiles(root_dir):
result = []
for path, dir_name, flist in os.walk(root_dir):
for f in flist:
fname = os.path.join(path, f)
if os.path.isfile(fname):
result.append(fname)
return result
# This code right now only deals with protein, but I will add functionality later for nucleotides.
# Just moving the project along here, but this is a critical flaw moving forward.
def do_parallel_blast(arg_tuple):
db, query_file, blast_result_folder, num_processors, eval_threshold = arg_tuple
out_file = "%s%s.txt" % (blast_result_folder, db.split('/')[-1].split('.')[0])
#print "db", db
#print "got here"
#cmd = "blastall -p tblastn -a %i -i %s -d %s -e %s -o %s -m 9" % (num_processors, query_file, db, eval_threshold, out_file)
#cmd = "blastall -p tblastn -a %i -i %s -d %s -e %s -o %s -m 9" % (1, query_file, db, eval_threshold, out_file)
#cmd = "blastall -p blastp -a %i -i %s -d %s -e %s -o %s -m 9" % (1, query_file, db, eval_threshold, out_file)
cmd = "blastall -p blastp -a %i -i %s -d %s -e %s -o %s -m 8" % (1, query_file, db, eval_threshold, out_file)
#print cmd
os.system( cmd )
#def parallel_blast(infile, query, folder, num_proc, e_val = '1e-10'):
def parallel_blast(database_folder, outfolder, filter_file, num_proc, query_file, e_val):
# you kinda have to trust me here, but having blast run on as many threads per CPU as you have total processors is fastest
# I have no idea why this is... ugh.
unfiltered_db_list = [i for i in returnRecursiveDirFiles(database_folder) if i.split('/')[-1].split('.')[-1] == 'ffc']
if filter_file == '':
db_list = unfiltered_db_list
else:
filter_list = [i.strip() for i in open(filter_file).readlines()]
db_list = [i for i in unfiltered_db_list if i.split('/')[-1].split('.')[0] in filter_list]
#print len(unfiltered_db_list), len(db_list)
#blast_arg_list = [(i, query_file, outfolder, num_proc, e_val) for i in db_list]
blast_arg_list = [(i, query_file, outfolder, 1, e_val) for i in db_list]
pool = Pool(processes = num_proc)
pool.map(do_parallel_blast, blast_arg_list)
def main():
start = time.time()
parsed_args = parser_code()
database_folder, outfolder, filter_file, num_proc, query_file, e_val = check_options(parsed_args)
print database_folder, outfolder, filter_file, num_proc, query_file, e_val
#parallel_blast(infile, query, folder, num_proc, e_val)
parallel_blast(database_folder, outfolder, filter_file, num_proc, query_file, e_val)
print time.time() - start
# ./blast_script.py -d ./db/ -o ./blast_result/ -q ./operon_query.fa
if __name__ == '__main__':
main()