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1 #!/usr/bin/python3
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2 import shutil, os, sys
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3
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4 # This scripts installs the pMLST database for using KMA
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5 # KMA should be installed before running this script
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6 # The scripts assumes that it is placed together with the pMLST scheme fasta files
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7 # First clone the repository: git clone https://bitbucket.org/genomicepidemiology/pmlst_db.git
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8
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9 # Check if executable kma_index program is installed, if not promt the user for path
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10
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11 interactive = True
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12 if len(sys.argv) >= 2:
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13 kma_index = sys.argv[1]
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14 if "non_interactive" in sys.argv:
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15 interactive = False
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16 else:
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17 kma_index = "kma_index"
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18
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19 while shutil.which(kma_index) is None:
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20 if not interactive:
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21 sys.exit("KMA index program, {}, does not exist or is not executable".format(kma_index))
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22 ans = input("Please input path to executable kma_index program or enter 'q'/'quit' to exit:")
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23 if ans == "q" or ans == "quit":
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24 print("Exiting!\n\n \
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25 Please install executable KMA programs in order to install this database.\n\n \
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26 KMA can be obtained from bitbucked:\n\n\
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27 git clone https://bitbucket.org/genomicepidemiology/kma.git\n\n\
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28 KMA programs must afterwards be compiled:\n\n\
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29 gcc -O3 -o kma KMA.c -lm -lpthread\n\
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30 gcc -O3 -o kma_index KMA_index.c -lm")
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31 sys.exit()
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32
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33 kma_index = ans
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34
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35 if shutil.which(kma_index) is None:
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36 print("Path, {}, is not an executable path. Please provide absolute path\n".format(ans))
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37
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38
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39 # Index databases
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40
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41
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42 # Use config_file to go through database files
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43 dirname = os.path.dirname(sys.argv[0])
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44
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45 config_file = open(os.path.join(dirname, "config"), "r")
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46 for line in config_file:
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47 if line.startswith("#"):
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48 continue
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49 else:
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50 line = line.rstrip().split("\t")
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51 scheme = line[0]
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52 f = os.path.join(dirname, scheme) + ".fsa"
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53 if not os.path.isfile(f):
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54 sys.exit("Database file '{}' does not exists".format(f))
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55 # for each dir index the fasta files
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56 os.system("{} -i {} -o {}".format(kma_index, f, os.path.join(dirname, scheme)))
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57
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58 config_file.close()
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59
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60 print("Done")
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61
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