slicing functionality for strings / Python suitability forbioinformatics

[Tom Anderson]

On Wed, 21 Sep 2005, Steven D'Aprano wrote:

> 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')

There's a special hell for people who override builtins.

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

It's definitely not currying - it doesn't create a new function. Currying 
would be:

def arraytype(kind):
 	def mkarray(value):
 		return array.array(kind, value)
 	return mkarray

chars = arraytype('c')
seq = chars("tacatcgtcgacgtcgatcagtaccc")

> 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:

Definitely - there are lots of things to know about DNA molecules or parts 
of them that aren't captured by the sequence.

tom

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