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

[joris meys]

I did, and that one works. But I can't specify here that I want only
100 positions from an alignment of 300 long for example. That's why I
have to do it myself.

I did lose the ampersand in the statement, but that didn't help one
bit. Next to that, my program is now complaining about unblessed
references when I put an alignment as an argument for a subroutine,
and I have no clue why.

Guess I'm not so OOP minded. I'll struggle on, thanks for the hints.
Cheers
Joris

On Sat, Oct 17, 2009 at 5:38 AM, Chris Fields <cjfields at illinois.edu> wrote:
> 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
>>>>
>>>>
>>>
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>
>