Biopython - Testing Techniques

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Biopython have extensive test script to test the software under different conditions to make sure that the software is bug-free. To run the test script, download the source code of the Biopython and then run the below command −

python run_tests.py

This will run all the test scripts and gives the following output −

Python version: 2.7.12 (v2.7.12:d33e0cf91556, Jun 26 2016, 12:10:39) 
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] 
Operating system: posix darwin 
test_Ace ... ok 
test_Affy ... ok 
test_AlignIO ... ok 
test_AlignIO_ClustalIO ... ok 
test_AlignIO_EmbossIO ... ok 
test_AlignIO_FastaIO ... ok 
test_AlignIO_MauveIO ... ok 
test_AlignIO_PhylipIO ... ok 
test_AlignIO_convert ... ok 
........................................... 
...........................................

We can also run individual test script as specified below −

python test_AlignIO.py

Conclusion

As we have learned, Biopython is one of the important software in the field of bioinformatics. Being written in python (easy to learn and write), It provides extensive functionality to deal with any computation and operation in the field of bioinformatics. It also provides easy and flexible interface to almost all the popular bioinformatics software to exploit the its functionality as well.

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