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