--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/db_pointfinder/INSTALL.py	Mon Jan 10 20:06:07 2022 +0000
@@ -0,0 +1,119 @@
+#!/usr/bin/python3
+import shutil
+import os
+import sys
+import tempfile
+import subprocess
+
+# 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 PointFinder species
+# directories
+#
+# First clone the repository:
+# git clone https://bitbucket.org/genomicepidemiology/pointfinder_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
+os.makedirs("kma_indexing", exist_ok=True)
+# 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_dir = line[0].strip()
+        # for each dir index the fasta files
+        os.system("{0} -i {1}/*.fsa -o {1}/{1}".format(kma_index, species_dir))
+
+config_file.close()
+
+eprint("Done")