[Bioperl-l] dnastatistics

[Liam Elbourne]

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.
>>
>> _________________________________________________________________
>> Hay tantos ordenadores como personas. ¡Descubre ahora cuál eres tú!
>> http://www.quepceres.com/
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> jason.stajich at gmail.com
> jason at bioperl.org
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

______________________________