[Bioperl-l] Bootstrapping positions in alignment - Utilities package

[Chris Fields]

Did you try bootstrap_replicates() from Bio::Align::Utilities?

chris

On Oct 16, 2009, at 9:51 PM, joris meys wrote:

> Thanks, but it's not really what I'm looking for. My alignments are
> flushed, so basically a matrix from which I need to select columns.
> These column indices come from an array with random numbers. It works
> with slice() from AlignI, I was just wondering if you could use an
> index of some sort like for an array. Something like
>
> $newaln = $oldaln [ @indices ]
>
> Thing is, I use this loop for it, but it doesn't want to work. $aln is
> a simpleAlign object
>
> use Bio::Align::Utilities qw(:all);
>
> my $out = Bio::SimpleAlign -> new;
> foreach (@indices){
>        my $temp = $aln -> slice($_ ,$_);
>        eval{$out = &cat($out,$temp)} or print $@ and $out = $temp;
>    }
> I use the eval construction to get passed a first error, but it
> doesn't work. I get as output :
>
> Undefined subroutine &main::cat called at...
> and then the result of the last round in the loop. I must be doing
> something wrong with the cat function from Align::Utilities.  But I
> have no clue what.
>
> The other function from the Utilities package, bootstrap_replicates,
> works just fine.
>
> Any tips are welcome
> Kind regards
> Joris
>
> On Sat, Oct 17, 2009 at 3:27 AM, Mark A. Jensen <maj at fortinbras.us>  
> wrote:
>> Hi Joris
>> You may find what you're looking for in this post:
>> http://lists.open-bio.org/pipermail/bioperl-l/2009-September/031292.html
>> cheers MAJ
>> ----- Original Message ----- From: "joris meys" <jorismeys at gmail.com>
>> To: <bioperl-l at lists.open-bio.org>
>> Sent: Friday, October 16, 2009 3:35 PM
>> Subject: [Bioperl-l] Bootstrapping positions in alignment
>>
>>
>>> Dear all,
>>>
>>> I'm using the packages AlignIO and AlignI to construct a  
>>> bootstrapping
>>> procedure on my alignments. There is a function slice() in AlignI I
>>> can use, but I actually need just a number of positions, not a  
>>> slice.
>>> Is there any other way of accessing the object so I can just specify
>>> one position?
>>>
>>> Thx in advance
>>> Joris
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l