Final presentation 20130625

1. Software Testing Project:
Testing csmap program
生醫電資所
黃建龍
2013.6.25

2. csmap - Conservation Score Mapper
● Mapping the given range of a sequence to
conservation scores of a chromosome.
● It used mmap, indexing and bisect module
for accessing data fastly.
● However, to determine which sites are on
the segments is complicated and error-
prone.

3. ● For display of dense, continuous data such
as GC percent, probability scores, and
transcriptome data.
● The conservation score is calculated with
whole genome multiple sequence
alignments.
● Segmented of many continuous data
Wiggle Track Format (WIG)

4. Wiggle Track Format (WIG)

5. file.seek(offset)
It moves the pointer to some other
part of the file so you can read or
write at that place.
e.g. seek(0) will move the pointer to
the beginning of file.

6. Testing Process
● Unit testing
○ Built-in unittest module (PyUnit)
○ Generation of test cases
● Coverage testing
○ coverage.py
● Mutation testing
○ PyMuTester

7. Unit testing
● Testing a class or individual function.
● Comparison of expected value and return
value.

8. unittest Module (PyUnit)
http://imsardine.wordpress.com/tech/unit-testing-in-python/
1. The test runner will
run that method prior
to each test.
2. The test runner will
invoke that method
after each test.

9. unittest Module (PyUnit)

10. Generation of Test Cases
● 5 regions.
● The length of each
region: 10
● The distance of two
neighboring regions: 10

11. Generation of Test Cases

12. Results

13. ● coverage.py (http://nedbatchelder.com/code/coverage/)
○ It monitors your program, noting which parts of the
code have been executed, then analyzes the source
to identify code that could have been executed but
was not.
Coverage testing

14. Coverage testing

15. HTML display

16. Bug fixes with test case 14.

17. Mutation testing
● It involves modifying a program's source
code in small ways.
● Mutations are based on well-defined
mutation operators (such as using the wrong
operator or variable name).
● It helps developers locate weaknesses in the
test cases used for the program.

18. PyMuTester

19. Results

20. Results
Total: 21
● Alive: 0 (0.0%)
● Killed 11 (52.4%)
● Unreachable: 10 (47.6%)

21. Conclusion
● Unit testing, coverage testing and mutation
testing were used in this study, and a bug
revealed under testing.
● The results of coverage testing and mutation
testing indicated that test cases were
insufficient or some of codes was
unreachable.