User:Jarle Pahr/Programming

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===Misc===
===Misc===
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http://www.python.org/dev/peps/
http://stackoverflow.com/questions/4583367/how-to-run-multiple-python-version-on-windows
http://stackoverflow.com/questions/4583367/how-to-run-multiple-python-version-on-windows

Revision as of 14:42, 7 April 2013

CodeEval - programming challenges: http://codeeval.com

http://software-carpentry.org/ - Learn scientific programming.

www.codecademy.com


https://www.researchgate.net/post/What_programming_language_is_best_for_a_bioinformatics_beginner

http://www.bin-co.com/blog/2008/03/learning-a-new-programming-language-the-hello-world-method/


Contents

Concepts/glossary:

  • Dynamic-link library: "DLLs provide a mechanism for shared code and data, allowing a developer of shared code/data to upgrade functionality without requiring applications to be re-linked or re-compiled." (Wikipedia).
  • Shell: "Software that provides and interface for users of an operating system to acess the services of a kernel" (Wikipedia). Typically, a graphical user interface (GUI) or a command-line interface (CLI). Examples: Windows Explorer (GUI), Windows Command Prompt (cmd.exe) (CLI), COMMAND.COM in DOS (CLI).
  • Shell script: "A script written for the shell, or command line interpreter, of an operating system." (Wikipedia)
  • IDE: Integrated Development Environment. Software application facilitating programming.
  • Garbage collection: Freeing of memory that is not used anymore.
  • Interpreter: A computer program that executes instructions written in a programming language.
  • Interpreted language: Language where programs can be run by an interpreter. Code must not be explicitly compilated (turned into an executable) in order to be run. MATLAB, Perl and Python are examples of interpreted languages. Interpreted programs typically run slower than compiled programs.
  • Scripting language: "a programming language that supports the writing of scripts, programs written for a software environment that automate the execution of tasks" (Wikipedia). Typical features are ease of use, OS facilities, interpreted from source code, loose structure.
  • Dynamic programming language: "a class of high-level programming languages that execute at runtime many common behaviors that other languages might perform during compilation, if at all." (Wikipedia). MATLAB, Perl, Python and R are dynamic programming languages. Not to be confused with dynamically typed language.
  • Type (Data Type): "lassification identifying one of various types of data, such as real-valued, integer or Boolean, that determines the possible values for that type; the operations that can be done on values of that type; the meaning of the data; and the way values of that type can be stored." (Wikipedia)
  • Type system: " a collection of rules that assign a property called a type to the various constructs—such as variables, expressions, functions or modules—a computer program is composed of." (Wikipedia)
  • Dynamically typed language: "A programming language is said to be dynamically typed when the majority of its type checking is performed at run-time as opposed to at compile-time. In dynamic typing values have types, but variables do not; that is, a variable can refer to a value of any type." (Wikipedia) Python and Perl are dynamically typed languages.
  • Run time: "the time during which a program is running (executing), in contrast to other phases of a program's lifecycle such as compile time, link time, load time, etc. A run-time error is detected after or during the execution of a program, whereas a compile-time error is detected by the compiler before the program is ever executed." (Wikipedia
  • Software library: " a collection of implementations of behavior, written in terms of a language, that has a well-defined interface by which the behavior is invoked.(...) Library code is organized in such a way that it can be used by multiple programs that have no connection to each other, while code that is part of a program is organized to only be used within that one program(...) A library is organized for the purposes of being reused by independent programs or sub-programs, and the user only needs to know the interface, and not the internal details of the library."
  • Imperative programming/Imperative language: "A programming paradigm that describes computation in terms of statements that change a program state(...). The term is used in opposition to declarative programming, which expresses what the program should accomplish without prescribing how to do it in terms of sequences of actions to be taken" (Wikipedia). Examples of imperative languages are C, C++, Java, COBOL and FORTRAN.

See http://stackoverflow.com/questions/602444/what-is-functional-declarative-and-imperative-programming

  • Object-oriented programming: "A programming paradigm that represents concepts as "objects" that have data fields (attributes that describe the object) and associated procedures known as methods." (Wikipedia)
  • Method

Languages

C

http://en.wikipedia.org/wiki/C_%28programming_language%29

Python

Official documentation

http://www.python.org/

Python standard library (Python 3.3): http://docs.python.org/3.3/library/


Python 2. 7 Documentation: http://docs.python.org/2.7/

Python 3.3 tutorial: http://docs.python.org/3.3/tutorial/

Python 3.3 glossary: http://docs.python.org/3.3/glossary.html#glossary

Python on Windows FAQ: http://docs.python.org/3.3/faq/windows.html

Python 3.3 Built-in functions: http://docs.python.org/3.3/library/functions.html#execfile

Learning Python

Beginning Python for bioinformatics Wiki: http://wiki.genedrift.org

http://www.codecademy.com/tracks/python

Bioinformatics Programming Using Python Practical Programming for Biological Data: http://shop.oreilly.com/product/9780596154516.do?

http://python-course.eu/

http://www.python-course.eu/matrix_arithmetic.php

http://www.daniweb.com/software-development/python/114

Misc

http://www.python.org/dev/peps/

http://stackoverflow.com/questions/4583367/how-to-run-multiple-python-version-on-windows

Article: Programming biological models in Python using PySB /doku.php?id=beginning_python_for_bioinformatics

http://ubuntuforums.org/showthread.php?t=127426

http://www.linuxtopia.org/online_books/programming_books/python_programming/python_ch20s05.html

http://www.syntagmatic.net/matrix-multiplication-in-python/

Stackoverflow - Python questions: http://stackoverflow.com/questions/tagged/python

Python books: http://wiki.python.org/moin/IntroductoryBooks

Python basic syntax: http://www.tutorialspoint.com/python/python_basic_syntax.htm

http://en.wikipedia.org/wiki/Python_syntax_and_semantics

Simple Python programs: http://wiki.python.org/moin/SimplePrograms

http://www.bin-co.com/blog/2008/03/python-hello-script/

About Python shells: http://python.about.com/od/programmingglossary/g/defshell.htm

Popular Python recipes: http://code.activestate.com/recipes/langs/python/

O'reilly Python devcenter: http://www.onlamp.com/python/

Differences between Python 2 and Python 3

  • Print is changed from a statement (print "something") to a function (print("something"))
  • raw_input() is replaced by input()

http://wiki.python.org/moin/Python2orPython3

http://docs.python.org/3/whatsnew/3.0.html

Q&A /How-tos

http://stackoverflow.com/questions/118260/how-to-start-idle-python-editor-without-using-the-shortcut-on-windows-vista

http://stackoverflow.com/questions/9831097/is-open-read-safe

http://stackoverflow.com/questions/3173915/modification-of-the-list-items-in-the-loop-python

http://stackoverflow.com/questions/4081217/how-to-modify-list-entries-during-for-loop

http://stackoverflow.com/questions/3591807/how-can-i-stop-python-exe-from-closing-immediatly-after-i-get-an-output

http://stackoverflow.com/questions/6513967/running-python-script-from-idle-on-windows-7-64-bit

http://stackoverflow.com/questions/1027714/how-to-execute-a-file-within-the-python-interpreter

http://stackoverflow.com/questions/2545397/converting-a-string-into-a-list-in-python

http://stackoverflow.com/questions/12336105/python-reverse-list

http://stackoverflow.com/questions/4481724/python-convert-list-of-char-into-string

Printing commands:

http://stackoverflow.com/questions/11266068/python-avoid-new-line-with-print-command

http://docs.python.org/2/tutorial/inputoutput.html

http://www.tutorialspoint.com/python/python_files_io.htm

Modules and libraries

NumPy & SciPy

SciPy is a packafe for scientific computing which depends on the NumPy package.

http://www.scipy.org/Topical_Software

SciPy: www.scipy.org/SciPy

Documentation: http://docs.scipy.org/doc/

http://www.scipy.org/more_about_SciPy

Projects using NumPy and/or SciPy: http://www.scipy.org/Projects

http://www.scipy.org/NumPy_for_Matlab_Users

http://scipy-central.org/

NumPy & SciPy FAQ: http://www.scipy.org/FAQ

Biology & Bioinformatics

Biopython:http://biopython.org/wiki/Main_Page

Biopython tutorial: http://biopython.org/DIST/docs/tutorial/Tutorial.html

Other

PyPI - Python package index: https://pypi.python.org/pypi

Python.org - useful modules: http://wiki.python.org/moin/UsefulModules

http://code.google.com/p/pythonxy/

http://matplotlib.org/


PyLab is part of matplotlib: http://stackoverflow.com/questions/12987624/confusion-between-numpy-scipy-matplotlib-and-pylab

iPython Notebook viewer: http://nbviewer.ipython.org/

Development environments

http://code.google.com/p/spyderlib/

http://ipython.org/

To launch iPython Notebook, write "ipython notebook" at the Windows command line (cmd.exe).

Distributions

EPD free edition: http://www.enthought.com/products/epd_free.php

Includes Python, iPython, IDLE, matplotlib, numpy and SciPy.

WinPython: https://code.google.com/p/winpython/

Includes NumPy, SciPy, matplotlib and Spyder.

Functions/methods

string.split("delimiter"): Splits a string into a list of strings. Ex: sequenc = ATGCA seq = sequence.split("G") --> seq = ['AT', 'CA']

list.append(x): Append object x to the end of list.

list.reverse(): Reverse order of elements in a list.

xrange():

"".join(list): Join list elements into a string.

Slice: slice(stop) slice(start, stop[, step])

"Returns a slice object representing the set of indices specified by range(start, stop, step)"

dictionary.item() Returns an array of tuples with each tuple consisting of a key/value pair from the dictionary:


Anonymous functions/lambda functions:

http://www.secnetix.de/olli/Python/lambda_functions.hawk

filter(function, iterable): Constructs a list from those elements of iterable for which the condition in function evaluates to true.

Keywords and statements

in :

with ... as


Indentation

http://stackoverflow.com/questions/119562/tabs-versus-spaces-in-python-programming

http://www.secnetix.de/olli/Python/block_indentation.hawk

http://stackoverflow.com/questions/5685406/inconsistent-use-of-tabs-and-spaces-in-indentation

http://stackoverflow.com/questions/1024435/howto-fix-python-indentation

Tips & Tricks

To stay in the Python interpreter environment after running a script, add - i before the script name: python -i script.py

A list can be reversed by the reverse function, or by list slicing with a negative stride:

backwards = my_list[::-1]

Perl

According to Wikipedia, Perl is "a high-level, general-purpose, interpreted, dynamic programming language."

Beginning Perl for Bioinformatics: http://shop.oreilly.com/product/9780596000806.do

http://www.cpan.org/

http://en.wikipedia.org/wiki/Outline_of_Perl


A "hash" in perl is the equivalent of a "dictionary" in Python.

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