By Mitchell Model, Model Mitchell, Tisdall James, James Tisdall

Robust, versatile, and straightforward to exploit, Python is a perfect language for development software program instruments and functions for all times technological know-how study and improvement. This designated publication exhibits you ways to software with Python, utilizing code examples taken without delay from bioinformatics. very quickly, you can be utilizing refined options and Python modules which are quite powerful for bioinformatics programming. Bioinformatics Programming utilizing Python is ideal for somebody concerned with bioinformatics -- researchers, aid employees, scholars, and software program builders drawn to writing bioinformatics functions. you will discover it helpful even if you already use Python, write code in one other language, or haven't any programming adventure in any respect. it is a very good self-instruction instrument, in addition to a convenient reference whilst dealing with the demanding situations of real-life programming initiatives. get to grips with Python's basics, together with how one can boost uncomplicated purposes use Python modules for trend matching, established textual content processing, on-line info retrieval, and database entry observe generalized styles that disguise a wide share of ways Python code is utilized in bioinformatics the right way to follow the foundations and methods of object-oriented programming enjoy the "tips and traps" part in every one bankruptcy

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Count('C')) / len(seq) A meaningful example of the use of this function would require a long base sequence, and then it would be difficult to tell whether the result was correct. 4 Assertions While developing code, it often happens that your functions get called with arguments of the wrong type or value. Depending on the details of the code, an invalid argument value may result in a Python error or a nonsensical result. Even worse, it might result in an apparently meaningful, but incorrect, result.

Changing multiple occurrences risks ending up with inconsistencies. Default Parameter Values You’ll often find that most calls to a certain function are likely to include the same value for a particular parameter. Frequently this value is something simple such as True, 0, or None. In such cases, Python provides a way to assign a default value to the parameter that will be used if no explicit value is included in a call to the function. As mentioned in the preceding chapter, some parameters of some functions are optional.

Consequently, docstrings have greater utility than comments. In particular, the help function looks at the docstring of a user-defined function together with its parameter list to generate a help description, as shown in Example 2-6. ”) Example 2-6. Help called on a user-defined function >>> help(validate_base_sequence) Help on function validate_base_sequence in module __main__: validate_base_sequence(base_sequence) Return True if the string base_sequence contains only upper- or lowercase T, C, A, and G characters, otherwise False Function definitions contain only statements.

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