[BioPython] a sequence set object in biopython?

[Giovanni Marco Dall'Olio]

On Thu, Nov 13, 2008 at 11:37 AM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> On Thu, Nov 13, 2008 at 12:16 AM, Giovanni Marco Dall'Olio wrote:
>>
>> I would prefer a SeqRecordSet object with a to_dict method :)
>
> OK, that is a style choice.
>
> BTW, you're using the word "Set" hear rather than "List", which could
> be misleading as in python sets have no order, but lists do.

Maybe the word 'SequencesPool' would be less misleading?
I don't have much confidence with English :(
The word List could also be misleading, because I was thinking about
an object that could act as a dictionary as well.


> Out of interest, why do you want to print out records to screen in a
> particular file format?  Why not just write them to a file?

just for debugging purposes - I wasn't expecting the blankline in the output.

> You don't like this:
>
> from Bio import SeqIO
> record_dict = SeqIO.to_dict(SeqIO.parse(handle, format))
>
> Well, I can live with it.  We *could* make the SeqIO.parse function
> always return a new object, a SeqRecordIterator which could have a
> to_dict() method in addition to the iteration interface - but this is
> overly complicated.

ok.. so I understand, if it would take too much work, nevermind.
I just thought it could have been an useful suggestion and sent it,
because otherwise I would have forgot about it :).

Cheers :)

> Peter
>



-- 
-----------------------------------------------------------

My Blog on Bioinformatics (italian): http://bioinfoblog.it