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.