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

joris meys jorismeys at gmail.com
Fri Oct 16 22:51:47 EDT 2009

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

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

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