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+++ b/resfinder/database_tests.md	Wed Dec 08 01:46:07 2021 +0000
@@ -0,0 +1,84 @@
+# 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))
+
+
+```