[Bioperl-l] Using Bio::Matrix::PhylipDist

[Iain Wallace]

Thanks for your help; The tests passed, and this showed my how I should 
use the function.

FYI:
The following from the test file works:
my $parser = new Bio::Matrix::IO(-format   => 'phylip'
                                  -program=> 'phylipdist',
                                  -file     => 't/data/phylipdist.out');
 my $matrix = $parser->next_matrix;



Jason Stajich wrote:

> Not sure what version of Bioperl you are using?
>
> Do the tests in  t/Matrix.t pass?
>
> Is your matrix file really populated?  Try running it with the test 
> file t/data/phylipdist.out instead.
>
> -jason
> -- 
> Jason Stajich
> jason.stajich at duke.edu
> http://www.duke.edu/~jes12/
>
> On Feb 28, 2005, at 6:23 AM, Iain Wallace wrote:
>
>> Hi all,
>>
>> I hope someone can help me.  I am trying to  read in a distance 
>> matrix using  Bio::Matrix::PhylipDist so that I can extract a subset 
>> of the matrix. However I am having some trouble reading in the Matrix.
>> I have tried a few different matrices so I don't think that is the 
>> problem. If any one has an idea on what I am doing wrong that would 
>> be great
>>
>> I have tried a few of the examples I found, but cann't seem to get 
>> them to work. It seems to be falling over at the $parser->next_matrix 
>> phase.
>>
>> ---Some of the examples I tried (from the module documentation) ----
>> from Bio::Matrix::IO::phylip
>> use Bio::Matrix::IO;
>>  my $parser = new Bio::Matrix::IO(-format   => 'phylip'
>>                                   -file     => 't/data/phylipdist.out');
>>  my $matrix = $parser->next_matrix;
>>
>> Error: Can't use an undefined value as an ARRAY reference at (full 
>> path)/Bio/Matrix/Generic.pm line 731
>>
>>
>> from Bio::Matrix::PhylipDist
>>
>> use Bio::Tools::Phylo::Phylip::ProtDist;
>>
>>  my $dist = Bio::Tools::Phylo::Phylip::ProtDist->new(
>>    -file=>"t/data/phylipdist.out",
>>    -program=>"ProtDist");
>>  #get specific entries
>>  my $distance_value = $dist->get_entry('ALPHA','BETA');
>>  my @columns        = $dist->get_column('ALPHA');
>>  my @rows           = $dist->get_row('BETA');
>>  my @diagonal       = $dist->get_diagonal();
>>
>>  #print the matrix in phylip numerical format
>>  print $dist->print_matrix;
>>
>> Error: Cann't locate object method "get_entry" via package.
>>
>> Then I modified the code, after looking at the  ProtDist.pm file
>> my $dist = $parser->next_matrix or die "could not parse matrix";
>> My script then dies at this point, not being able to parse the matrix.
>>
>>
>> Thanks
>>
>> Iain
>>
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