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diff resfinder/database_tests.md @ 0:a16d245332d6 draft default tip
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author | dcouvin |
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date | Wed, 08 Dec 2021 01:46:07 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ 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)) + + +```