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

[joris meys]

Found the unblessed reference problem, but with or without ampersand,
I get the same error out of the eval. It doesn't find the function
somehow, and I'm baffled about why.

Cheers
Joris

On Sat, Oct 17, 2009 at 2:48 PM, joris meys <jorismeys at gmail.com> wrote:
> 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
>>>>> _______________________________________________
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>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>
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>>
>>
>