slicing functionality for strings / Python suitability forbioinformatics

[Steven D'Aprano]

On Mon, 19 Sep 2005 19:40:12 -0700, jbperez808 wrote:

> Having to do an array.array('c',...):
> 
>   >>> x=array.array('c','ATCTGACGTC')
>   >>> x[1:9:2]=array.array('c','AAAA')
>   >>> x.tostring()
>   'AACAGACATC'
> 
> is a bit klunkier than one would want, but I guess
> the efficient performance is the silver lining here.

There are a number of ways to streamline that. The simplest is to merely
create an alias to array.array:

from array import array as str

Then you can say x = str('c', 'ATCTGACGTC').

A little more sophisticated would be to use currying:

def str(value):
    return array.array('c', value)

x = str('ATCTGACGTC')

although to be frank I'm not sure that something as simple as this
deserves to be dignified with the name currying.


Lastly, you could create a wrapper class that implements everything you
want. For a serious application, this is probably what you want to do
anyway:

class DNA_Sequence:
    alphabet = 'ACGT'

    def __init__(self, value):
        for c in value:
            if c not in self.__class__.alphabet:
                raise ValueError('Illegal character "%s".' % c)
        self.value = array.array('c', value)

    def __repr__(self):
        return self.value.tostring()

and so on. Obviously you will need more work than this, and it may be
possible to subclass array directly. 


-- 
Steven.