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biopython, doctest and makefiles

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Giovanni Marco Dall'Olio
Giovanni Marco Dall'Olio

This is a very short 30-minutes talk that I gave to a barcelona python developers meeting. It explain a proposal to use doctest for biopython documentation (and in general, in bioinformatics). It also contains an introduction and the use of automated build tools in bioinformatics, like make and scons.

Technology
1 of 22
Barcelona Python Developers Seminars biopython, doctest and makefiles
This is me ,[object Object],[object Object],[object Object],[object Object]
Intro ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
BioPython – some use cases ,[object Object],[object Object],[object Object],[object Object],[object Object]
BioPython – use cases ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
BioPython documentation ,[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],doctest ,[object Object],Example of say_hello's usage function's docstring (everything in green)
The docstring ,[object Object],>>> help (say_hello) Help on function say_hello in module __main__: say_hello(name) print hello <name> to the screen example: >>> say_hello('Albert Einstein') hello Albert Einstein!!!
doctest – how does it works ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
doctest - examples ,[object Object]
doctest – file parsing example ,[object Object],[object Object],[object Object]
Choose good examples ,[object Object],[object Object],[object Object]
Doctest – Pros and Cons ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Bioinformatics – a different approach ,[object Object],[object Object],[object Object],[object Object]
What is a makefile? ,[object Object],[object Object],[object Object]
Simplest Makefile example ,[object Object]
Makefiles – Pros ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Make - Cons ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
A more complicated Makefile ,[object Object],[object Object],[object Object],[object Object]
Thanks for the attention! Did you like the talk?
BioPython – use cases ,[object Object],[object Object],[object Object]
Doctest – a closer look ,[object Object],[object Object],[object Object],[object Object],normal doc example of function usage expected output body of the function call to the doctest module new function definition

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