Mercurial > repos > dcouvin > resfinder4

comparison resfinder/db_resfinder/INSTALL.py @ 0:55051a9bc58d draft default tip

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author dcouvin
date Mon, 10 Jan 2022 20:06:07 +0000
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-1:000000000000 0:55051a9bc58d
1 #!/usr/bin/python3
2 import shutil
3 import os
4 import sys
5 import tempfile
6 import subprocess
7
8 # TODO:
9 # Make script independent of current working directory
10 # Make script able to store indexed files in a directory not named
11 # 'kma_indexing'
12
13 # This scripts installs the PointFinder database for using KMA
14 # KMA should be installed before running this script
15 # The scripts assumes that it is placed together with the ResFinder species
16 # directories
17 #
18 # First clone the repository:
19 # git clone https://bitbucket.org/genomicepidemiology/resfinder_db.git
20
21 # Check if executable kma_index program is installed, if not promt the user for
22 # path
23
24
25 # Function for easy error printing
26 def eprint(*args, **kwargs):
27 print(*args, file=sys.stderr, **kwargs)
28
29
30 # KMA version
31 #KMA_VERSION = "latest"
32
33
34 interactive = True
35 if len(sys.argv) >= 2:
36 kma_index = sys.argv[1]
37 if "non_interactive" in sys.argv:
38 interactive = False
39 else:
40 kma_index = "kma_index"
41
42 print(str(sys.argv))
43
44 while shutil.which(kma_index) is None:
45 eprint("KMA index program, {}, does not exist or is not executable"
46 .format(kma_index))
47 ans = None
48 if(interactive):
49 ans = input("Please input path to executable kma_index program or"
50 "choose one of the options below:\n"
51 "\t1. Install KMA using make, index db, then remove KMA.\n"
52 "\t2. Exit\n")
53
54 if(ans == "2" or ans == "q" or ans == "quit" or ans == "exit"):
55 eprint("Exiting!\n\n"
56 "Please install executable KMA programs in order to install"
57 "this database.\n\n"
58 "KMA can be obtained from bitbucked:\n\n"
59 "git clone"
60 "https://bitbucket.org/genomicepidemiology/kma.git"
61 )
62 sys.exit()
63
64 if(ans == "1" or ans is None):
65 if(shutil.which("git") is None):
66 sys.exit("Attempt to automatically install KMA failed.\n"
67 "git does not exist or is not executable.")
68 org_dir = os.getcwd()
69
70 # Create temporary directory
71 tempdir = tempfile.TemporaryDirectory()
72 os.chdir(tempdir.name)
73
74 try:
75 subprocess.run(
76 ["git", "clone",
77 "https://bitbucket.org/genomicepidemiology/kma.git"],
78 check=True)
79 os.chdir("kma")
80 except subprocess.CalledProcessError:
81 eprint("Installation in temporary directory with make failed "
82 "at the git cloning step")
83 os.chdir(org_dir)
84
85 try:
86 subprocess.run(["make"])
87 except subprocess.CalledProcessError:
88 eprint("Installation in temporary directory with make failed "
89 "at the make step.")
90 os.chdir(org_dir)
91
92 kma_index = "{}/kma/kma_index".format(tempdir.name)
93 os.chdir(org_dir)
94 if shutil.which(kma_index) is None:
95 eprint("Installation in temporary directory with make failed "
96 "at the test step.")
97 os.chdir(org_dir)
98 kma_index = "kma_index"
99 if(not interactive):
100 ans = "2"
101
102 if(ans is not None and ans != "1" and ans != "2"):
103 kma_index = ans
104 if shutil.which(kma_index) is None:
105 eprint("Path, {}, is not an executable path. Please provide "
106 "absolute path\n".format(ans))
107
108
109 # Index databases
110
111 # Use config_file to go through database dirs
112 config_file = open("config", "r")
113 for line in config_file:
114 if line.startswith("#"):
115 continue
116 else:
117 line = line.rstrip().split("\t")
118 drug = line[0].strip()
119 # for each dir index the fasta files
120 os.system("{0} -i {1}.fsa -o ./{1}".format(kma_index, drug))
121 os.system("{0} -i *.fsa -o ./all".format(kma_index))
122
123 config_file.close()
124
125 eprint("Done")