+
−#!/usr/bin/python3
+
−import shutil, os, sys
+
−
+
−# This scripts installs the PlasmidFinder database for using KMA
+
−# KMA should be installed before running this script
+
−# The scripts is assumed to be located together with plasmidfinder's '.fsa' files
+
−#
+
−# First clone the repository: git clone https://bitbucket.org/genomicepidemiology/plasmidfinder_db.git
+
−
+
−# Check if executable kma_index program is installed, if not promt the user for path
+
−
+
−interactive = True
+
−if len(sys.argv) >= 2:
+
−    kma_index = sys.argv[1]
+
−    if "non_interactive" in sys.argv:
+
−        interactive = False
+
−else:
+
−    kma_index = "kma_index"
+
−
+
−while shutil.which(kma_index) is None:
+
−    if not interactive:
+
−        sys.exit("KMA index program, {}, does not exist or is not executable".format(kma_index))
+
−    ans = input("Please input path to executable kma_index program or enter 'q'/'quit' to exit:")
+
−    if ans == "q" or ans == "quit":
+
−        print("Exiting!\n\n \
+
−               Please install executable KMA programs in order to install this database.\n\n \
+
−               KMA can be obtained from bitbucked:\n\n\
+
−               git clone https://bitbucket.org/genomicepidemiology/kma.git\n\n\
+
−               KMA programs must afterwards be compiled:\n\n\
+
−               gcc -O3 -o kma KMA.c -lm -lpthread\n\
+
−               gcc -O3 -o kma_index KMA_index.c -lm")
+
−        sys.exit()
+
−
+
−    kma_index = ans
+
−
+
−    if shutil.which(kma_index) is None:
+
−        print("Path, {}, is not an executable path. Please provide absolute path\n".format(ans))
+
−
+
−
+
−# Index databases
+
−
+
−# Use config_file to go through database dirs
+
−config_file = open("config", "r")
+
−for line in config_file:
+
−    if line.startswith("#"):
+
−        continue
+
−    else:
+
−        line = line.rstrip().split("\t")
+
−        species = line[0] 
+
−        # for each dir index the fasta files
+
−        os.system("{0} -i {1}.fsa -o {1}".format(kma_index, species))
+
−config_file.close() 
+
−
+
−print("Done")