diff pmlst/pmlst_db/INSTALL.py @ 0:cfab64885f66 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pmlst/pmlst_db/INSTALL.py	Mon Sep 06 18:27:45 2021 +0000
@@ -0,0 +1,61 @@
+#!/usr/bin/python3
+import shutil, os, sys
+
+# This scripts installs the pMLST database for using KMA
+# KMA should be installed before running this script
+# The scripts assumes that it is placed together with the pMLST scheme fasta files
+# First clone the repository: git clone https://bitbucket.org/genomicepidemiology/pmlst_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 files
+dirname = os.path.dirname(sys.argv[0])
+
+config_file = open(os.path.join(dirname, "config"), "r")
+for line in config_file:
+    if line.startswith("#"):
+        continue
+    else:
+        line = line.rstrip().split("\t")
+        scheme = line[0] 
+        f = os.path.join(dirname, scheme) + ".fsa"
+        if not os.path.isfile(f):
+            sys.exit("Database file '{}' does not exists".format(f))
+        # for each dir index the fasta files
+        os.system("{} -i {} -o {}".format(kma_index, f, os.path.join(dirname, scheme)))
+
+config_file.close() 
+
+print("Done")
+