[Bioperl-l] dnastatistics

Tue Sep 22 11:12:38 UTC 2009

Thanks Liam-- I think the discrepancy between dnadist and the
module is worth making a bug report for- can you do that and
include the data (or part of it) you were using?
Jason, is that work really underway, or should someone pick up
that ball?
----- Original Message ----- 
From: "Liam Elbourne" <lelbourn at science.mq.edu.au>
To: "Jason Stajich" <jason at bioperl.org>
Cc: "Mark A. Jensen" <maj at fortinbras.us>; <bioperl-l at bioperl.org>; "Jose ." 
<joseguillin at hotmail.com>
Sent: Tuesday, September 22, 2009 3:14 AM
Subject: [Bioperl-l] dnastatistics

So I also had no problem running the code as written by Jose (Bioperl
1.6.0, perl 5.10), but in the documentation for DNAStatistics it says:

"The routines are not well tested and do contain errors at this point.
Work is underway to correct them, but do not expect this code to give
you the right answer currently!"!

So I'm using dnadist (as I think the documentation recommends), and it
does produce different numbers to $stats->distance(-).

I tried write_matrix from Bio::Matrix::IO - got a message saying it
hasn't been implemented yet?

And if Jose hasn't already found it, try Data::Dumper; it will change
your life....

Regards,
Liam.

On 15/09/2009, at 3:54 AM, Jason Stajich wrote:

> 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 $jcmatrix->print_matrix;
>>
>> And the file 'e1_output_uno_solo.fas' has the following sequences:
>>
>>> A
>> GGTTATCTCAACAACTGTCACC--GTGGGCGCTGGTCATTGGTACGGGTGAACGAGAGTT
>> AAACGGTCGTTAACCATAGAAACAAAACACACTGCACCTTAACTCACTGAATAGTTGACG
>> GTCTGCCTCAGGGCTTGAGACAACGGATGGATCTAAACTCATGCTGTAGCCTATCAAACT
>> TAGCCCCAGGGTACTTCCGTCCCTAGCCTCGCTACAAGGCCAGAAAGGGTTTTGAAGTCT
>> ACTCACTGTGACCAGCGGTCTAGTCAGGTTATGCTTCGGCACAAAACCTCAGAATCGGTA
>> ACCAGCCACTACACGAACTGAAATCAAATCGCGGGAGGTGGTCCATCTTTGTCCACGCTG
>> CGATGATTGGGTTGCTTTATAGTCTAGCTGCAAGGTTTTGCGTTCTGGTGGGAAGCGGSubject:  Re: 
>> [Bioperl-l] Bio/Align/DNAStatistics.html
> print$jcmatrix->print_maCA
>> 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
>
>
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