Mercurial > repos > dcouvin > resfinder4
comparison resfinder/database_tests.md @ 0:55051a9bc58d draft default tip
Uploaded
author | dcouvin |
---|---|
date | Mon, 10 Jan 2022 20:06:07 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:55051a9bc58d |
---|---|
1 # PhenoDB Test | |
2 | |
3 It is not necessary to test the validity of a database that has just been | |
4 cloned. The main reason for running tests are to test a database that has been | |
5 altered. The tests run are by no mean exhaustive and will not guarantee a valid | |
6 database. | |
7 | |
8 This file will test the validity of the databases installed in the default | |
9 locations. These are: | |
10 - [resfinder app dir]/db_resfinder | |
11 - [resfinder app dir]/db_pointfinder | |
12 Where [resfinder app dir] is the root directory of the ResFinder application. | |
13 You will find the "run_resfinder.py" file in this directory. | |
14 | |
15 Run the following command to test validity of databases. | |
16 | |
17 ```bash | |
18 | |
19 python3 -m doctest database_test.md | |
20 | |
21 ``` | |
22 | |
23 *Note*: Change the database locations to be tested by changing the first three | |
24 lines of the python code below in this file. | |
25 | |
26 ```python | |
27 | |
28 >>> db_resfinder = "db_resfinder/" | |
29 >>> db_pointfinder = "db_pointfinder/" | |
30 ``` | |
31 | |
32 ## Test phenotype.txt and resistens-overview.txt files | |
33 | |
34 ```python | |
35 | |
36 >>> from cge.phenotype2genotype.res_profile import PhenoDB | |
37 | |
38 >>> phenodb = PhenoDB( | |
39 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
40 ... acquired_file="{}phenotypes.txt".format(db_resfinder), | |
41 ... point_file="{}campylobacter/resistens-overview.txt".format(db_pointfinder), | |
42 | |
43 >>> phenodb = PhenoDB( | |
44 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
45 ... point_file="{}enterococcus_faecalis/resistens-overview.txt".format(db_pointfinder)) | |
46 | |
47 >>> phenodb = PhenoDB( | |
48 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
49 ... point_file="{}enterococcus_faecium/resistens-overview.txt".format(db_pointfinder)) | |
50 | |
51 >>> phenodb = PhenoDB( | |
52 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
53 ... point_file="{}escherichia_coli/resistens-overview.txt".format(db_pointfinder)) | |
54 | |
55 >>> phenodb = PhenoDB( | |
56 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
57 ... point_file="{}helicobacter_pylori/resistens-overview.txt".format(db_pointfinder)) | |
58 | |
59 >>> phenodb = PhenoDB( | |
60 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
61 ... point_file="{}klebsiella/resistens-overview.txt".format(db_pointfinder)) | |
62 | |
63 >>> phenodb = PhenoDB( | |
64 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
65 ... point_file="{}mycobacterium_tuberculosis/resistens-overview.txt".format(db_pointfinder)) | |
66 | |
67 >>> phenodb = PhenoDB( | |
68 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
69 ... point_file="{}neisseria_gonorrhoeae/resistens-overview.txt".format(db_pointfinder)) | |
70 | |
71 >>> phenodb = PhenoDB( | |
72 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
73 ... point_file="{}plasmodium_falciparum/resistens-overview.txt".format(db_pointfinder)) | |
74 | |
75 >>> phenodb = PhenoDB( | |
76 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
77 ... point_file="{}salmonella/resistens-overview.txt".format(db_pointfinder)) | |
78 | |
79 >>> phenodb = PhenoDB( | |
80 ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), | |
81 ... point_file="{}staphylococcus_aureus/resistens-overview.txt".format(db_pointfinder)) | |
82 | |
83 | |
84 ``` |