[Biopython] Sequence object "find" is still case specific?

[Fields, Christopher J]

On Mar 3, 2013, at 2:39 PM, Peter Cock <p.j.a.cock at googlemail.com>
 wrote:

> On Sun, Mar 3, 2013 at 7:13 PM, hari jayaram <harijay at gmail.com> wrote:
> ...
>> or
>> 
>> It just silently converts it all to the case of the Unambiguous_DNA
>> specification and then all "find" and "search" works regardless of case on
>> this internal representation which is just "DNA".
> 
> You mean if an all upper case alphabet is used, silently switch
> the sequence to upper case? And vice verse for lower case?
> That seems to0 magic/implicit, so I'd not support that.

A note/warning: Peter's right, I've been bitten by such magic (on the Bioperl end :) a number of times.  We're intending on removing such magic in v2.  It's best to throw an exception and let someone know why it doesn't work than try 'helping' and end up misunderstanding the user's intent.

> 
> Peter


chris