Open writing projects/Sage and cython a brief introduction

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This is a quick introduction to [[http://www.sagemath.org/index.html Sage]], a powerful new computational platform that builds on the strengths of Python.  This article was directly inspired by Julius B. Lucks' [[http://openwetware.org/wiki/Julius_B._Lucks/Projects/Python_All_A_Scientist_Needs "Python: All A Scientist Needs"]]; I recommend reading it first as it explains some of the attractions of Python and biopython.   
This is a quick introduction to [[http://www.sagemath.org/index.html Sage]], a powerful new computational platform that builds on the strengths of Python.  This article was directly inspired by Julius B. Lucks' [[http://openwetware.org/wiki/Julius_B._Lucks/Projects/Python_All_A_Scientist_Needs "Python: All A Scientist Needs"]]; I recommend reading it first as it explains some of the attractions of Python and biopython.   
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Sage () is a free and open-source project for computation of all sorts that uses Python as its primary language and "glue".  One of the goals of Sage is to provide a viable free and open-source alternative to Matlab, Maple, and Mathematica.  Sage unifies a great deal of open-source mathematical and statistical software; it includes biopython as an optional package and the statistics language R by default.
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Sage is a free and open-source project for computation of all sorts that uses Python as its primary language and "glue".  One of the goals of Sage is to provide a viable free and open-source alternative to Matlab, Maple, and Mathematica.  Sage unifies a great deal of open-source mathematical and statistical software; it includes biopython as an optional package and the statistics language R by default.
== Sage notebook interface ==
== Sage notebook interface ==
(TODO: notebook interface screenshots, different computers, good 2-d graphics)
(TODO: notebook interface screenshots, different computers, good 2-d graphics)
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 +
A key feature of Sage is its notebook web-browser interface. 
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Jose Unpingco has made a [[http://sage.math.washington.edu/home/wdj/expository/unpingco/ good short introductory video]] on the notebook interface that may help get a sense of what its like.
<syntax type="python">
<syntax type="python">

Revision as of 16:18, 1 May 2008

Contents

Work in progress

Please check back later for the final version...

Abstract

This is a quick introduction to [Sage], a powerful new computational platform that builds on the strengths of Python. This article was directly inspired by Julius B. Lucks' ["Python: All A Scientist Needs"]; I recommend reading it first as it explains some of the attractions of Python and biopython.

Sage is a free and open-source project for computation of all sorts that uses Python as its primary language and "glue". One of the goals of Sage is to provide a viable free and open-source alternative to Matlab, Maple, and Mathematica. Sage unifies a great deal of open-source mathematical and statistical software; it includes biopython as an optional package and the statistics language R by default.

Sage notebook interface

(TODO: notebook interface screenshots, different computers, good 2-d graphics)

A key feature of Sage is its notebook web-browser interface.

Jose Unpingco has made a [good short introductory video] on the notebook interface that may help get a sense of what its like.

<syntax type="python"> def PStoRE(PrositePattern):

   """
   Converts a PROSITE regular expression to a python r.e.
   """
   rePattern = PrositePattern
   rePattern = rePattern.replace('-',)
   rePattern = rePattern.replace(' ',)
   rePattern = rePattern.replace('x','.')
   rePattern = rePattern.replace('{','[^')
   rePattern = rePattern.replace('}',']')
   rePattern = rePattern.replace('(','{')
   rePattern = rePattern.replace(')','}')
   return rePattern

from Bio import Fasta import re import urllib2 as U @interact def re_scan(fasta_file_url = 'http://www.d.umn.edu/~mhampton/PlasProtsRef.fa', pat = input_box('G - x - P - [AG] - x(2) - [LIVM] - x - [IV] ', type = str, width = 60)):

   re_pat = re.compile(PStoRE(pat))
   parser = Fasta.RecordParser()
   prot_file = U.urlopen(fasta_file_url)
   fasta_iterator = Fasta.Iterator(prot_file, parser = parser)
   for record in fasta_iterator:
       matches = re_pat.findall(record.sequence)
       if len(matches) != 0:
           html(record.title)
           html(matches)
           print 

</syntax> Image:rebrowse1.png

Cython

Sage initially used an alternative to SWIG (described in Julius's article) called Pyrex to compile Python code to C when performance concerns demanded it. Because they needed to extend Pyrex in various ways, they created a friendly fork of Pyrex called "Cython". I believe it is fair to say that Cython is the easiest way to create C code in Python.

(TODO: example of Cython usage)

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