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#!/usr/bin/python3
import shutil
import os
import sys
import tempfile
import subprocess
# TODO:
# Make script independent of current working directory
# Make script able to store indexed files in a directory not named
# 'kma_indexing'
# This scripts installs the PointFinder database for using KMA
# KMA should be installed before running this script
# The scripts assumes that it is placed together with the ResFinder species
# directories
#
# First clone the repository:
# git clone https://bitbucket.org/genomicepidemiology/resfinder_db.git
# Check if executable kma_index program is installed, if not promt the user for
# path
# Function for easy error printing
def eprint(*args, **kwargs):
print(*args, file=sys.stderr, **kwargs)
# KMA version
KMA_VERSION = "1.0.1"
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"
print(str(sys.argv))
while shutil.which(kma_index) is None:
eprint("KMA index program, {}, does not exist or is not executable"
.format(kma_index))
ans = None
if(interactive):
ans = input("Please input path to executable kma_index program or"
"choose one of the options below:\n"
"\t1. Install KMA using make, index db, then remove KMA.\n"
"\t2. Exit\n")
if(ans == "2" or ans == "q" or ans == "quit" or ans == "exit"):
eprint("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 -b {:s} "
"https://bitbucket.org/genomicepidemiology/kma.git"
.format(KMA_VERSION))
sys.exit()
if(ans == "1" or ans is None):
if(shutil.which("git") is None):
sys.exit("Attempt to automatically install KMA failed.\n"
"git does not exist or is not executable.")
org_dir = os.getcwd()
# Create temporary directory
tempdir = tempfile.TemporaryDirectory()
os.chdir(tempdir.name)
try:
subprocess.run(
["git", "clone", "-b", KMA_VERSION,
"https://bitbucket.org/genomicepidemiology/kma.git"],
check=True)
os.chdir("kma")
except subprocess.CalledProcessError:
eprint("Installation in temporary directory with make failed "
"at the git cloning step")
os.chdir(org_dir)
try:
subprocess.run(["make"])
except subprocess.CalledProcessError:
eprint("Installation in temporary directory with make failed "
"at the make step.")
os.chdir(org_dir)
kma_index = "{}/kma/kma_index".format(tempdir.name)
os.chdir(org_dir)
if shutil.which(kma_index) is None:
eprint("Installation in temporary directory with make failed "
"at the test step.")
os.chdir(org_dir)
kma_index = "kma_index"
if(not interactive):
ans = "2"
if(ans is not None and ans != "1" and ans != "2"):
kma_index = ans
if shutil.which(kma_index) is None:
eprint("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")
drug = line[0].strip()
# for each dir index the fasta files
os.system("{0} -i {1}.fsa -o ./{1}".format(kma_index, drug))
os.system("{0} -i *.fsa -o ./all".format(kma_index))
config_file.close()
eprint("Done")
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