Open writing projects/Sage and cython a brief introduction

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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.

The @interact command in the Sage notebook provides an easy way to make simple GUIs to explore data. In the example below, a user can enter the URL of a fasta-formatted protein file and a PROSITE-style regular expression. Using biopython and the "re" module of python we can search for and display matches to the pattern. For this screenshot, I used proteins from the malaria-causing Plasmodium falciparum and a fragment of the transthyretin pattern (Prosite PS00768). This is just for illustrative purposes - I do not claim any significance for these matches.

<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>

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)