BIO::PHYLO TREE GENERATOR AND IO

[willingtone odhiambo]

 I wish to ask for assistance,i downloaded n installed bio::phylo on both windows and bio-linux os however am not able to run script for tree viewing am getting the error cant locate tree generator and IO.Any advice on what i should do.Thanks in advance .

willingtone.

[Rutger Vos]

Dear Willingtone,

this sounds more like a general problem in installing Perl modules. Could you please explain how you did the installation and where Bio::Phylo now resides in your system?

Thanks,

Rutger

On Tue, Oct 28, 2014 at 8:36 PM, willingtone odhiambo <willin...@gmail.com> wrote:

 I wish to ask for assistance,i downloaded n installed bio::phylo on both windows and bio-linux os however am not able to run script for tree viewing am getting the error cant locate tree generator and IO.Any advice on what i should do.Thanks in advance .

willingtone.

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[willingtone odhiambo]

Hi Mr.Rugter,

Am glad to hear from you,i downloaded the Bio::Phylo package manually from the web,then i transfered the file to directory "temp" that i had created in The OS(c:).I however had to unzip the file,i  used the instructions on the READme to install using the command prompt.the make command i used was "dmake".Once i ahad located the file c:\temp\Bio-phylo-0.58>perl.makefilr.PL
dmake
dmaketest
dmakeinstall

Thats how i did it.

Regards
willingtone

[Rutger Vos]

Hi Willingtone,

what you need to do is make sure that Perl can find where you install libraries. The error that you are getting indicates that it is not currently finding them. This means that you may have to do something like setting an environment variable (called PERL5LIB), or add a location when you run a script (e.g. perl -I/location/of/bio/phylo scriptname.pl), or add that location inside your script (e.g. "use lib '/location/of/bio/phylo'"). 

In any case neither the problem nor any of the solutions have directly to do with Bio::Phylo but with how you have Perl configured on your computer. It might make sense to search the web for the (exact) error message you are getting, because there will be many tutorials and forum posts about how to solve this problem.

Best wishes,

Rutger

--

[Willingtone]

Hi Dr.Rutger,
Thanks for your input and guidance,i followed through and managed to change the environment variable and its now picking the bio::phylo software,am how stuck on some scrpts that are not running through like the use of url to abtain the phyogenetic files for viewing.could you advance? Thanks


Regards
Willingtone.

---

From: Rutger Vos
Sent: ‎30/‎10/‎2014 22:17
To: bio-...@googlegroups.com
Subject: Re: BIO::PHYLO TREE GENERATOR AND IO

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[Rutger Vos]

Hi Willingtone,

what do you mean by "not running"? I can only help if I can see the code and the error.

Thanks,

Rutger

[willingtone odhiambo]

Hi Dr Rutger,

My apology for not responding late and for not giving the full information,i have to admit that am anew beginner in using Bio::phylo,i read your paper (vos 2011),i intend to use Bio::phylo to view phylogenetic trees and  also for mapping the trees,i have afile from clustalw omega for some seq that i had send for multi-alignment,am trying to get view the tree via Bio::phylo the script is:
use lib'/home/foobar/code';
use Bio::Phylo::generator;
my $string = "new 1.newick";
my $forest = parse( -format => 'newick', -string => $string );
print $forest;
print ref $forest;
 foreach my $tree ( @{ $forest=>get_entities } ) {
      print ref $tree;

      foreach my $node ( @{ $tree=>get_entities } ) {
      print $node;
          print ref $node;

      }

 the error is Microsoft Windows [Version 6.2.9200]
(c) 2012 Microsoft Corporation. All rights reserved.

C:\Users\willingtone>Documents\tyrial.pl
-------------------------- EXCEPTION ----------------------------
Message: Can't locate Math/Random.pm in @INC (@INC contains: /home/foobar/code C
:/Perl/site/lib C:/Perl/lib .) at C:/Perl/site/lib/Bio/Phylo/Util/CONSTANT.pm li
ne 296.


An exception of type Bio::Phylo::Util::Exceptions::ExtensionError
was thrown.

This kind of error happens when an extension module can not be
loaded.

Refer to the Bio::Phylo::Util::Exceptions documentation for more
information.
------------------------- STACK TRACE ---------------------------
STACK: Bio::Phylo::Util::CONSTANT::looks_like_class('Math::Random') called at C:
/Perl/site/lib/Bio/Phylo/Util/Dependency.pm line 9
STACK: Bio::Phylo::Util::Dependency::import('Bio::Phylo::Util::Dependency', 'Mat
h::Random') called at C:/Perl/site/lib/Bio/Phylo/generator.pm line 6
STACK: Bio::Phylo::Generator::BEGIN() called at C:/Perl/site/lib/Bio/Phylo/gener
ator.pm line 6
STACK: (eval)() called at C:/Perl/site/lib/Bio/Phylo/generator.pm line 6
STACK: (eval)() called at C:\Users\willingtone\Documents\tyrial.pl line 2
STACK: main::BEGIN() called at C:/Perl/site/lib/Bio/Phylo/generator.pm line 6
STACK: (eval)() called at C:/Perl/site/lib/Bio/Phylo/generator.pm line 6

-----------------------------------------------------------------
BEGIN failed--compilation aborted at C:/Perl/site/lib/Bio/Phylo/generator.pm lin
e 6.
Compilation failed in require at C:\Users\willingtone\Documents\tyrial.pl line 2
.
BEGIN failed--compilation aborted at C:\Users\willingtone\Documents\tyrial.pl li
ne 2.

C:\Users\willingtone>

kindly assist and please also advice on how ione can obtaion data from website directly to view the phylogenetic trees.i followed the example in your paper but it couldnt extra the data.

Regards
willingtone

..our lives are in Gods hands,only HE figures and configures our days..

[Rutger Vos]

Hi Willingtone,

the error message indicates that the module Math::Random is not installed on your system. This module is used by Bio::Phylo::Generator (which you are using in your code). If you wish to simulate phylogenies by using Bio::Phylo::Generator (because that's what that module is for) you will need to install Math::Random first.

Best wishes,

Rutger