Scientific computing using Python

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422–1423.

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

www.biocodershub.net/community/hitchhikers-guide-to-biopython-seqrecords/

http://telliott99.blogspot.no/

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/

PyDoc: http://docs.python.org/2/library/pydoc

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/ (See iPython)

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

Function definition:

http://docs.python.org/3/tutorial/controlflow.html#defining-functions

Docstrings:

http://www.python.org/dev/peps/pep-0257/

String methods:

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

string.find() :

string.strip([chars]): "Return a copy of the string with the leading and trailing characters removed." Character to be removed are specified by [chars]. If no argument given, the chars argument defaults to removing whitespace.

Array/list methods:

Enumerate: http://docs.python.org/2/library/functions.html#enumerate

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

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

range / xrange(start, stop[,step]): returns a list of plain integers [start, start + step, start + 2 * step, ...]

"".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:

map(function,iterable): Apply function to every item in iterable and return the result.

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.

sum(): From official Python documentation: "Sums start and the items of an iterable from left to right and returns the total. Start defaults to 0"

Input/Output (I/O):

From http://www.python.org/dev/peps/pep-0234/ :

" Because the file iterator uses an internal buffer, mixing this

   with other file operations (e.g. file.readline()) doesn't work
   right:

Fore more on iteration over files, see:

http://www.bogotobogo.com/python/python_iterators.php

Class-related functions:

isinstance.

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

Classes

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

http://www.cafepy.com/article/python_types_and_objects/python_types_and_objects.html

http://www.w3resource.com/python/python-object-classes.php

http://en.wikibooks.org/wiki/Python_Programming/Classes

A simple class inheritance example: http://www.daniweb.com/software-development/python/code/216596/a-simple-class-inheritance-example-python

An introduction to classes and inheritance in Python: http://www.jesshamrick.com/2011/05/18/an-introduction-to-classes-and-inheritance-in-python/

http://en.wikibooks.org/wiki/Think_Python/Inheritance

Inheritance in Python: http://www.packtpub.com/article/inheritance-python

Creating instances:

http://stackoverflow.com/questions/2136760/creating-an-instance-of-a-class-with-a-variable-in-python

Class scope:

http://www.codecademy.com/courses/python-intermediate-en-WL8e4/1/2#

Super:

Things to know about Python Super: http://www.artima.com/weblogs/viewpost.jsp?thread=236275

Method Resolution Order:

http://www.cafepy.com/article/python_attributes_and_methods/ch02.html

http://python-history.blogspot.no/2010/06/method-resolution-order.html

http://luisartola.com/software/2010/method-resolution-order-blues/

Misc.:

http://stackoverflow.com/questions/3625726/python-error-nameerror-global-name-self-is-not-defined-when-calling-another

http://stackoverflow.com/questions/2424451/compound-assignment-to-python-class-and-instance-variables

http://www.python.org/doc/essays/ppt/acm-ws/sld051.htm

Input/Output

Execution

Executing command line commands:

import os
os.system("script.py argument")

Opening files:

os.startfile(filepath)

Command line input

http://www.daniweb.com/software-development/python/threads/12326/how-to-do-input-in-python

http://stackoverflow.com/questions/70797/python-and-user-input

Opening & Reading files

Open file object methods:

.read() : Returns one line as a string

.readlines() Reads the entire file, returns a list of every line with each line as one string element.

By using a with as block, the file will be automatically closed when the block ends:

with open('workfile', 'r') as f:
  read_data = f.read()

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

http://en.wikibooks.org/wiki/Python_Programming/Files

Pickle: Module which converts objects to strings.

http://www.diveintopython.net/file_handling/file_objects.html

Interfacing

http://www.pythonforbeginners.com/python-on-the-web/how-to-access-various-web-services-in-python/

Tips & Tricks

Execute python scripts online: http://www.compileonline.com/execute_python_online.php

Get current working directory:

import os
os.getcwd()

Set current working directory:

os.chdir(aPath)

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]

Calling file from interpreter command line:

command = "find /tmp -name '*.jpg'"
subprocess.call(command.split())

29 common errors: http://pythonforbiologists.com/index.php/29-common-beginner-python-errors-on-one-page/

Style guide: https://www.draftable.com/compare/9spTfcM?utm_source=buffer&utm_campaign=Buffer&utm_content=buffere23fd&utm_medium=twitter

http://pythonarticles.com/?utm_content=buffer08069&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

Common newbie mistakes part 1: http://blog.amir.rachum.com/post/54770419679/python-common-newbie-mistakes-part-1

Developing your own scientific Python code: http://www.linuxjournal.com/content/developing-your-own-scientific-python-code?utm_content=buffer1d018&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer

About iterations: http://nedbatchelder.com/text/iter/iter.html#13

Python on Android

http://kivy.org/#home

http://google-opensource.blogspot.no/2009/06/introducing-android-scripting.html

http://code.google.com/p/android-scripting/

http://qpython.com/

https://ep2013.europython.eu/conference/talks/developing-android-apps-completely-in-python

Packaging

http://guide.python-distribute.org/introduction.html

http://stackoverflow.com/questions/6344076/differences-between-distribute-distutils-setuptools-and-distutils2

https://python-packaging-user-guide.readthedocs.org/en/latest/index.html

http://answers.yahoo.com/question/index?qid=20110705223937AA8vFXz

Installing Python modules: http://docs.python.org/3/install/index.html

Distributing Python modules: http://docs.python.org/3/distutils/index.html

PIP

http://stackoverflow.com/questions/4750806/how-to-install-pip-on-windows

http://en.wikipedia.org/wiki/Pip_%28Python%29

http://stackoverflow.com/questions/3849762/python-3-easy-install-pip-and-pypi

easy_install

module bundled with setup_tools

http://peak.telecommunity.com/DevCenter/EasyInstall

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

Distribute

Setuptools

Replaced by Distribute

Python Package index (PyPi)

https://pypi.python.org/pypi

Error handling

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

http://www.linuxtopia.org/online_books/programming_books/python_programming/python_ch17s03.html

http://stackoverflow.com/questions/2052390/how-do-i-manually-throw-raise-an-exception-in-python

http://docs.python.org/3.3/tutorial/errors.html http://stackoverflow.com/questions/1313812/raise-exception-vs-return-none-in-python-functions

http://stackoverflow.com/questions/730764/try-catch-in-python-how-to-properly-ignore-exceptions

Examples

Get index of list element:

    for i,v in enumerate(line_segments):
      print i, v

Use of zip:

x = [1,2,3]
y = [2,3,4]
f = zip(x,y)

String formatting

http://stackoverflow.com/questions/3089038/python-not-all-of-arguments-converted-during-string-formatting

http://stackoverflow.com/questions/7351270/control-a-print-format-when-printing-a-list-in-python

http://stackoverflow.com/questions/15575359/print-list-elements-with-comprehension-python

http://stackoverflow.com/questions/7568627/using-python-string-formatting-with-lists

http://www.velocityreviews.com/forums/t677371-type-float-problem.html

http://stackoverflow.com/questions/9535954/python-printing-lists-as-tabular-data

http://stackoverflow.com/questions/3018295/how-do-i-print-a-table-in-python

http://stackoverflow.com/questions/12078802/python-how-do-i-dynamically-print-a-table-of-strings-in-the-terminal

http://stackoverflow.com/questions/2762058/format-all-elements-of-a-list

http://stackoverflow.com/questions/4440516/in-python-is-there-an-elegant-way-to-print-a-list-in-a-custom-format-without-ex

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

http://www.shocksolution.com/2011/11/python-string-format-examples/

Division operations

http://www.linuxtopia.org/online_books/programming_books/python_programming/python_ch05s06.html

Plotting & animation

Several ways to create an animation:

Using easyviz:

import scitools.easyviz as ev
counter = 0
for i in range(10):
   counter +=1
   y = 0.1*i*x
   ev.plot(x,y,'go', axis=[0,100,0,100],savefig ='jpa%04d.png' % counter)    
   ev.show()
   time.sleep(0.5)

ev.movie('jpa*.png')

Using matplotlib.animation:

http://matplotlib.org/api/animation_api.html

http://jakevdp.github.io/blog/2012/08/18/matplotlib-animation-tutorial/

http://stackoverflow.com/questions/16732379/stop-start-pause-in-python-matplotlib-animation

http://scipyscriptrepo.com/wp/?p=9

Easyviz

http://folk.uio.no/hpl/easyviz/easyviz.html

http://scitools.googlecode.com/hg-history/e7dc9172a38b8c0c7963315be46b36084d9edd87/doc/api/sphinx-html/movie.html

http://code.google.com/p/scitools/wiki/EasyvizDocumentation

User:Jarle Pahr/Python

Scientific computing using Python

Official documentation

Learning Python

Misc

Differences between Python 2 and Python 3

Q&A /How-tos

Data strutures

Dictionaries

Lists

Tuples

Arrays

Named tuples

Applications

Modules and libraries

NumPy & SciPy

Biology & Bioinformatics