[Biopython] shuffle sequences

[George Devaniranjan]

Thanks Iddo and João,
I think this works and it seems to shuffle the sequence well to
differentiate between the original and shuffled (very diff scores for
alignment.)

George

On Tue, Jun 7, 2011 at 11:11 AM, Iddo Friedberg <idoerg at gmail.com> wrote:

> probably a good solution wouls be to convert to  a list and then back to a
> string (or a Seq object).
>
> To shuffle w:
> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
> wl=list(w)
> random.shuffle(wl)
> w=''.join(wl)
>
> And with a Seq object:
> myseq=Seq('KVFGRCELAAAMKRHGL')
> lms = list(myseq)
> random.shuffle(lms)
> myseq = Seq(''.join(lms))
>
>
> On Tue, Jun 7, 2011 at 11:01 AM, George Devaniranjan <
> devaniranjan at gmail.com> wrote:
>
>> Hello João,
>>
>> Thanks for the answer but I am confused--"new sequence object with that"
>> so I still need to create a seq object?
>> I tried this ...
>> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>>
>> I was thinking if it would be possible to have FOR loop and loop throught
>> the entire sequence then shuffle it and then write the shuffled list
>> (going
>> though it one by one using another FOR loop) to a seq object.
>>
>> Thank you,
>> George
>>
>> On Tue, Jun 7, 2011 at 10:46 AM, João Rodrigues <anaryin at gmail.com>
>> wrote:
>>
>> > Hey George,
>> >
>> > random.shuffle works on lists or other datatypes that support item
>> > assignment. Therefore, neither a string nor Seq will work. I would
>> extract
>> > the sequence out of Seq and build a new sequence object with that.
>> >
>> > Cheers,
>> >
>> > João [...] Rodrigues
>> > http://nmr.chem.uu.nl/~joao
>> >
>> >
>> >
>> > On Tue, Jun 7, 2011 at 3:39 PM, George Devaniranjan <
>> > devaniranjan at gmail.com> wrote:
>> >
>> >> Hello everyone,
>> >> I need to 'shuffle' a sequence so that I can calculate the statistical
>> >> alignment scores--I tried the random.shuffle opetion but it does not
>> seem
>> >> to
>> >> work
>> >>
>> >> I defined the sequence as a string like the following
>> >>
>> >> w="KVYGRCELAAAMKRHGLDKYQGYSLGNWVCAAKFE"
>> >> random.shuffle(w)
>> >>
>> >>
>> >> also like this...
>> >> my_protein=IUPAC.protein
>> >> from Bio.Seq import Seq
>> >> myseq=Seq('KVFGRCELAAAMKRHGL', my_protein)
>> >>
>> >> random.shuffle(myseq)
>> >>
>> >> Both don't seem to work--where am I going wrong?
>> >>
>> >> Thanks a lot,
>> >> George
>> >> _______________________________________________
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>> >> http://lists.open-bio.org/mailman/listinfo/biopython
>> >>
>> >
>> >
>>
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>
>
>
> --
> Iddo Friedberg
> http://iddo-friedberg.net/contact.html
>