Mercurial > repos > dcouvin > resfinder4
view resfinder/database_tests.md @ 0:55051a9bc58d draft default tip
Uploaded
author | dcouvin |
---|---|
date | Mon, 10 Jan 2022 20:06:07 +0000 |
parents | |
children |
line wrap: on
line source
# PhenoDB Test It is not necessary to test the validity of a database that has just been cloned. The main reason for running tests are to test a database that has been altered. The tests run are by no mean exhaustive and will not guarantee a valid database. This file will test the validity of the databases installed in the default locations. These are: - [resfinder app dir]/db_resfinder - [resfinder app dir]/db_pointfinder Where [resfinder app dir] is the root directory of the ResFinder application. You will find the "run_resfinder.py" file in this directory. Run the following command to test validity of databases. ```bash python3 -m doctest database_test.md ``` *Note*: Change the database locations to be tested by changing the first three lines of the python code below in this file. ```python >>> db_resfinder = "db_resfinder/" >>> db_pointfinder = "db_pointfinder/" ``` ## Test phenotype.txt and resistens-overview.txt files ```python >>> from cge.phenotype2genotype.res_profile import PhenoDB >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... acquired_file="{}phenotypes.txt".format(db_resfinder), ... point_file="{}campylobacter/resistens-overview.txt".format(db_pointfinder), >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}enterococcus_faecalis/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}enterococcus_faecium/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}escherichia_coli/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}helicobacter_pylori/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}klebsiella/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}mycobacterium_tuberculosis/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}neisseria_gonorrhoeae/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}plasmodium_falciparum/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}salmonella/resistens-overview.txt".format(db_pointfinder)) >>> phenodb = PhenoDB( ... abclassdef_file="{}antibiotic_classes.txt".format(db_resfinder), ... point_file="{}staphylococcus_aureus/resistens-overview.txt".format(db_pointfinder)) ```