[Bioperl-l] Bio/Align/DNAStatistics.html print$jcmatrix->print_matrix;

[Jason Stajich]

Yeah it seems like more of a bioperl problem -- possible that the  
older code didn't recognize 'jukes-cantor' but you can try the  
abbreviation 'jc' -- better to just upgrade tho!

This isn't the cause of the problem but I would also encourage use of  
Bio::Matrix::IO for printing the matrix (use the 'write_matrix'  
function) rather than print_matrix on the matrix itsself.

-jason
On Sep 14, 2009, at 10:00 AM, Mark A. Jensen wrote:

> Hi Jose--
> I don't get any problem with your script as written. You should  
> upgrade to
> BioPerl 1.6 and try again.
> The "unblessed reference" is $jcmatrix. It may be undef for some  
> reason.
> MAJ
> ----- Original Message ----- From: "Jose ." <joseguillin at hotmail.com>
> To: <bioperl-l at bioperl.org>
> Sent: Monday, September 14, 2009 8:48 AM
> Subject: [Bioperl-l] Bio/Align/DNAStatistics.html print$jcmatrix- 
> >print_matrix;
>
>
>
>
>
> Hello,
>
> I'm trying to use Bio::Align::DNAStatistics, but I get the following  
> message:
>
> Can't call method "print_matrix" on unblessed reference at Tree.pl  
> line 32, <GEN0> line 44.
>
> Other modules do work, such us Bio::SimpleAlign;
>
>
>
>
> My code is basically a modification of the code I found in http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/Align/DNAStatistics.html 
> , as it is as follows:
>
> use strict;
> use Bio::AlignIO;
> use Bio::Align::DNAStatistics;
>
>
> my $stats = Bio::Align::DNAStatistics->new();
>
> my $alignin = Bio::AlignIO->new(-file => 'e1_output_uno_solo.fas',
>                           -format => 'fasta');
> my $aln = $alignin->next_aln;
>
> my $jcmatrix = $stats-> distance (-align => $aln,
>                 -method => 'Jukes-Cantor');
>
> print $jcmatrix->print_matrix;
>
> And the file 'e1_output_uno_solo.fas' has the following sequences:
>
>> A
> GGTTATCTCAACAACTGTCACC--GTGGGCGCTGGTCATTGGTACGGGTGAACGAGAGTT
> AAACGGTCGTTAACCATAGAAACAAAACACACTGCACCTTAACTCACTGAATAGTTGACG
> GTCTGCCTCAGGGCTTGAGACAACGGATGGATCTAAACTCATGCTGTAGCCTATCAAACT
> TAGCCCCAGGGTACTTCCGTCCCTAGCCTCGCTACAAGGCCAGAAAGGGTTTTGAAGTCT
> ACTCACTGTGACCAGCGGTCTAGTCAGGTTATGCTTCGGCACAAAACCTCAGAATCGGTA
> ACCAGCCACTACACGAACTGAAATCAAATCGCGGGAGGTGGTCCATCTTTGTCCACGCTG
> CGATGATTGGGTTGCTTTATAGTCTAGCTGCAAGGTTTTGCGTTCTGGTGGGAAGCGGCA
> TCCAAGGGGTTGACTCCGCTCGTTTATAACATGCCTTGGGCCTCCATGGTGAGTCGCAAC
> GTCAGCGTAGGCCTAGACGGCT
>
>> B
> GGATATCTCGACAACTTTTAGC--CTGGGCGCTTGGCATTGGTACACGTGACTTGCAGTT
> AAAGGGTCGTTATACATAGAATCACTACCCAC--CAGGCGAACTCGCTGGAGAGCTGAGG
> GTCACCCTCAGCGGTTGAGTTAACTGCTCGATGTTAACCGATGTTGGATCATAGGTAACT
> TATCCTCAGTGTTCCTCTGTCCCTAGACTGGCTACAGGGCTACACCGGGTTTGAGGGGAT
> ACTGACTGTTTTCAGCGGTAGTGTAAGTGTATGGTCCAACCCAAGGGTTCATGACCGGTA
> AACTGCCCGTTCCCGCATTGAAATCAAATTGCAGGAGTTGGTACTTATTTGTCAACCTTA
> CGATGATTGGGATGCATTTTAGTCGGGCTGGGCGGATTTGCGATCTGGGTGGAAGAGAGA
> TGCATGGGGCTAACTCGTCTTGGTGAGTACCGGCATTGCACCGCAATGGACCGCCAAAAC
> ATAAGAGTAGGTCGGGATGGCA
>
>> C
> GCTTATCTCAACAACCGACACGAAGTCGTCGCAGGTCAATGGTACACGTGAATTGAAGTC
> ATAAGATCAGTAATGATCGAACCACCAAACCCTTAACCTCGACTCACGCGATAGCCGAGG
> GTCTGCCTCCAGGGTTGATTTAAAGGTTCTATTTAAGACCGTTTTCGATCATAGGTTACT
> TATCCCCAGAGTTCTACCGTCGTGAGAATGGCTACAAGGCTAGAATAGGTTTTAGGGT-T
> ACTTACGGTCTGCAGCCGTATTGTGAGGTTATGGTCCGGCCCTAGGCGTCATGACCGATA
> ATCAGCCCCTACCTGAAATGAAATCAAATCGCGGGAGTTGGTACTTATCTGTCAACGTTG
> CGATGATGGGGATACATGTTGGTCTACCGCGACGGACTAGCGATCACGGGGGAAGCGGAT
> TGCCCGGTGGTGACTCGACACGTTTAAAACCTGCCTGGTTCCCGCATGGATCGTCACAAC
> GTATGTGCAGGTCGAAACGAGT
>
>> D
> CGTGATCGCAACAACTGTCACC--GTGGGCGCTGGCCGTTGGACCACGTGAAATGCTGTT
> AAACGATCGTTCACCATAGAACCACTACACTCTTCACCTCAACCCGCGGGACAGGTGATG
> GTGTCCCCCAGGGGTTGAGTGAACGGCTCGATGTAAACCCATGTTCGATCATAGGTAACG
> TAGCCCCAGGGTGATTCCGTTCCTAAACTGGTTACAAGGCTAAAACGTGTTTTAGAGTAT
> AATGACTGTCTACGGCGGTATTGTGATGTTATCATCCGTCCCTAGGCGTGGCGACCGTTA
> AACAGCCTCTTCCCTAACTGATATCTAATCGTAGGAGTTGCTACGCATTTGTCAACGCAG
> CGATGATGGTGATGCATCTTAATCTAGCTGG----TTTTTTGATCTCGGGTGACGCAGAT
> AGTCAGGGGTTGACTCGCGTCGTTTGAAACGTGCCTTGCTCCTCAATGGACCCTCCGAAC
> CTAAGAGTAGCTCGACACGGCT
>
>
>
> I think the $aln object is OK, as I can use it with SimpleAlign.
>
> Moreover, if I write
>         print $jcmatrix;
> instead of
>         print $jcmatrix->print_matrix;
> I get the memory reference, as normal===> ARRAY(0x859f08)
>
> So my question is:
>
> Why do I have an unblessed reference?
>
> Can't call method "print_matrix" on unblessed reference at Tree.pl  
> line 32, <GEN0> line 44.
>
> Thank you very much in advance.
>
> Jose G.
>
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org