bioprov.tests package

Submodules

bioprov.tests.test_bioprov_imports module

Testing module for the package BioProv.

Tests include:
  • Imports;

  • Class generation and methods.

bioprov.tests.test_bioprov_imports.test_import_bioprov()

Test if the package can be imported correctly. :return: ImportError if not able to import.

bioprov.tests.test_bioprov_imports.test_import_classes_and_functions()

Test if all classes and functions can be imported correctly. :return: ImportError if not able to import

bioprov.tests.test_bioprov_imports.test_import_packages()

Test if supplementary packages can be imported correctly. :return: ImportError if not able to import

bioprov.tests.test_bioprov_integration module

Integration testing for drafting new ideas.

bioprov.tests.test_bioprov_integration.test_CLI()
bioprov.tests.test_bioprov_integration.test_integration(debug=False)

Tests an example pipeline of running Prodigal. :return:

bioprov.tests.test_bioprov_programs module

Testing for the programs package.

bioprov.tests.test_bioprov_programs.test_blastn()
bioprov.tests.test_bioprov_programs.test_blastp()
bioprov.tests.test_bioprov_programs.test_diamond()
bioprov.tests.test_bioprov_programs.test_fasttree()
bioprov.tests.test_bioprov_programs.test_kaiju()

Testing the ‘kaiju’ program. :return:

bioprov.tests.test_bioprov_programs.test_kaiju2table()

Testing the ‘kaiju2table’ program :return:

bioprov.tests.test_bioprov_programs.test_kallisto()
bioprov.tests.test_bioprov_programs.test_mafft()
bioprov.tests.test_bioprov_programs.test_muscle()
bioprov.tests.test_bioprov_programs.test_prodigal()

Testing the ‘prodigal’ program. :return:

bioprov.tests.test_bioprov_programs.test_prokka()

Testing the ‘prokka’ program. :return:

bioprov.tests.test_bioprov_workflows module

Testing for the workflows package.

bioprov.tests.test_bioprov_workflows.test_blastn_workflow()
bioprov.tests.test_bioprov_workflows.test_genome_annotation()

Tests the ‘genome_annotation’ workflow with the ‘prodigal’ step. :return:

bioprov.tests.test_bioprov_workflows.test_kaiju_workflow()

Tests the ‘kaiju’ workflow. :return:

bioprov.tests.test_src_config module

Testing for the Config module.

bioprov.tests.test_src_config.test_BioProvDB()
bioprov.tests.test_src_config.test_Config()

Testing for the Config class :return:

bioprov.tests.test_src_file module

Testing for the File module.

bioprov.tests.test_src_file.test_File_and_Directory()
Tests objects in the File module:
  • existing File instance

  • non-existing File instance

  • get_size(), convert_bytes()

Returns

bioprov.tests.test_src_file.test_SeqFile()

Tests the SeqFile constructor. :return:

bioprov.tests.test_src_main module

Testing for the bioprov.src.main module.
Tests the following classes:
  • Program

  • Parameter

  • Run

  • Sample

  • Project

Also tests JSON and tab-delimited serializer methods.

bioprov.tests.test_src_main.create_sample(attributes_)
bioprov.tests.test_src_main.test_Parameter()

Testing for the Parameter class. :return:

bioprov.tests.test_src_main.test_Program()

Testing for the Program class. :return:

bioprov.tests.test_src_main.test_Project()

Testing for the Project class. :return:

bioprov.tests.test_src_main.test_Run()

Testing for the Run class. :return:

bioprov.tests.test_src_main.test_Sample()

Testing for the Sample class. :return:

bioprov.tests.test_src_main.test_empty_runs_attr()

Tests if, when runs is empty, dependent attributes return None

bioprov.tests.test_src_main.test_from_df()

Testing for the from and read_csv functions. :return:

bioprov.tests.test_src_main.test_generate_param_str()

Testing for generate_param_str() function. :return:

bioprov.tests.test_src_main.test_json_Sample()

Testing for JSON methods for the Sample class. :return:

bioprov.tests.test_src_main.test_parse_params()

Testing for the parse_params() function. :return:

bioprov.tests.test_src_main.test_preset_extra_flags()
bioprov.tests.test_src_main.test_project_json_and_prov()

bioprov.tests.test_src_prov module

Testing for prov module.
  • BioProvDocument class

bioprov.tests.test_src_prov.test_BioProvDocument()

Tests the construction of an instance of BioProvDocument. :return:

bioprov.tests.test_src_prov.test_EnvProv()

Tests the construction of an instance of Environment. :return:

Module contents

Init file for the tests/ package.