Beautiful data

I think this is the most beautiful plot the has ever been made to represent GC content in a sequence. 

Using GenBank sequences as the dataset, I used BioPython, matplotlib to analyze and draw the plot. Can't post the source here since it'll give away what I'm up to but you can always ask if you're interested.

Python web programming using web.py

For the first time in a long while, I had the opportunity to have a free day. So what did I do with it? I coded of course.

I started exploring how to do web programming with Python and stumbled on web.py. At first it didn't seem very trivial but the more I tinkered around with the sample codes, the more I got interested.

So I wrote some code that prints the reverse complement of the a DNA sequence.

import web
from web import form
import re

render = web.template.render('templates/')

urls = ('/revcom', 'index')
app = web.application(urls, globals())

myform = form.Form( 
    form.Textbox('Sequence',
                 form.notnull,
                 form.Validator('Must be a G,A,T or C', lambda x: re.match('^[gatcGATC\s]+$', x) )
                 ,size=30)
    )

def revcom(seq):
    from Bio.Seq import Seq
    from Bio.Alphabet import IUPAC

    seq = str(seq).replace(' ', '')
    myseq = Seq(str(seq), IUPAC.unambiguous_dna)
    return str(myseq.reverse_complement())

class index: 
    def GET(self): 
        form = myform()
        return render.formtest(form)

    def POST(self): 
        form = myform() 
        if not form.validates(): 
            return render.formtest(form)
        else:
            return revcom(form['Sequence'].value)

if __name__=="__main__":
    web.internalerror = web.debugerror
    app.run()

Seems to be running OK. I hope I have time to follow on this. 

BMW 1M

BMW 1M, a photo by <kent> on Flickr.

Someday you will be mine.

Reboot

Hello World! Again.