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1 #!/usr/bin/python3
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2 import shutil
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3 import os
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4 import sys
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5 import tempfile
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6 import subprocess
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7
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8 # This scripts installs the PointFinder database for using KMA
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9 # KMA should be installed before running this script
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10 # The scripts assumes that it is placed together with the PointFinder species
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11 # directories
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12 #
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13 # First clone the repository:
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14 # git clone https://bitbucket.org/genomicepidemiology/pointfinder_db.git
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15
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16 # Check if executable kma_index program is installed, if not promt the user for
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17 # path
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18
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19
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20 # Function for easy error printing
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21 def eprint(*args, **kwargs):
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22 print(*args, file=sys.stderr, **kwargs)
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23
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24
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25 # KMA version
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26 KMA_VERSION = "1.0.1"
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27
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28
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29 interactive = True
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30 if len(sys.argv) >= 2:
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31 kma_index = sys.argv[1]
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32 if "non_interactive" in sys.argv:
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33 interactive = False
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34 else:
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35 kma_index = "kma_index"
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36
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37 print(str(sys.argv))
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38
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39 while shutil.which(kma_index) is None:
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40 eprint("KMA index program, {}, does not exist or is not executable"
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41 .format(kma_index))
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42 ans = None
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43 if(interactive):
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44 ans = input("Please input path to executable kma_index program or"
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45 "choose one of the options below:\n"
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46 "\t1. Install KMA using make, index db, then remove KMA.\n"
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47 "\t2. Exit\n")
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48
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49 if(ans == "2" or ans == "q" or ans == "quit" or ans == "exit"):
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50 eprint("Exiting!\n\n"
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51 "Please install executable KMA programs in order to install"
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52 "this database.\n\n"
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53 "KMA can be obtained from bitbucked:\n\n"
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54 "git clone -b {:s} "
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55 "https://bitbucket.org/genomicepidemiology/kma.git"
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56 .format(KMA_VERSION))
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57 sys.exit()
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58
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59 if(ans == "1" or ans is None):
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60 if(shutil.which("git") is None):
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61 sys.exit("Attempt to automatically install KMA failed.\n"
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62 "git does not exist or is not executable.")
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63 org_dir = os.getcwd()
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64
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65 # Create temporary directory
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66 tempdir = tempfile.TemporaryDirectory()
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67 os.chdir(tempdir.name)
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68
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69 try:
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70 subprocess.run(
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71 ["git", "clone", "-b", KMA_VERSION,
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72 "https://bitbucket.org/genomicepidemiology/kma.git"],
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73 check=True)
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74 os.chdir("kma")
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75 except subprocess.CalledProcessError:
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76 eprint("Installation in temporary directory with make failed "
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77 "at the git cloning step")
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78 os.chdir(org_dir)
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79
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80 try:
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81 subprocess.run(["make"])
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82 except subprocess.CalledProcessError:
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83 eprint("Installation in temporary directory with make failed "
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84 "at the make step.")
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85 os.chdir(org_dir)
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86
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87 kma_index = "{}/kma/kma_index".format(tempdir.name)
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88 os.chdir(org_dir)
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89 if shutil.which(kma_index) is None:
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90 eprint("Installation in temporary directory with make failed "
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91 "at the test step.")
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92 os.chdir(org_dir)
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93 kma_index = "kma_index"
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94 if(not interactive):
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95 ans = "2"
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96
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97 if(ans is not None and ans != "1" and ans != "2"):
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98 kma_index = ans
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99 if shutil.which(kma_index) is None:
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100 eprint("Path, {}, is not an executable path. Please provide "
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101 "absolute path\n".format(ans))
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102
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103
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104 # Index databases
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105 os.makedirs("kma_indexing", exist_ok=True)
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106 # Use config_file to go through database dirs
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107 config_file = open("config", "r")
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108 for line in config_file:
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109 if line.startswith("#"):
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110 continue
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111 else:
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112 line = line.rstrip().split("\t")
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113 species_dir = line[0].strip()
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114 # for each dir index the fasta files
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115 os.system("{0} -i {1}/*.fsa -o {1}/{1}".format(kma_index, species_dir))
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116
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117 config_file.close()
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118
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119 eprint("Done")
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