[Bioperl-l] Bio::Tree:Statistics parsimony question

[Mark A. Jensen]

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----- Original Message ----- 
From: "Mark A. Jensen" <maj at fortinbras.us>
To: "Chris" <coldmeadow at gmail.com>
Sent: Friday, October 23, 2009 8:14 AM
Subject: Re: [Bioperl-l] Bio::Tree:Statistics parsimony question


> Hi Chris, 
> 
> looks like you could simply do
> 
> @ps = map { $obj->ps($tree, $_) } @seq;
> 
> or into a hash %ps with tags as keys:
> 
> @ps{@seq} = map { $obj->ps($tree,$_) } @seq;
> 
> cheers MAJ
> ----- Original Message ----- 
> From: "Chris" <coldmeadow at gmail.com>
> To: <bioperl-l at bioperl.org>
> Sent: Friday, October 23, 2009 1:10 AM
> Subject: [Bioperl-l] Bio::Tree:Statistics parsimony question
> 
> 
>> Hello,
>> I have been able to use the ps() method in Bio::Tree::Statistics to calulate
>> the parsimony for tag values from a tree if they are strings.
>> 
>> This is the way I have been implementing the method:
>> 
>> my $obj = Bio::Tree::Statistics->new();
>> my $pars = $obj->ps($tree,'seq');
>> print "Parsimony = $pars \n";
>> 
>> Is it possible to do so if they are an array?
>> 
>> say I have an array @seq = qw(A,A,C,G), I can add these as values to a leaf
>> node of a tree using;
>> 
>> foreach my $char (@seq){
>>   $node->add_tag_value('seq',$char);
>> }
>> 
>> Does anybody have a suggestion to get the parsimony for each label of the
>> array of labels for such a tree ?
>> 
>> Thanks in advance,
>> Chris.
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>> 
>>