Bio::TreeIO::nexus.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP

SYNOPSIS

   use Bio::TreeIO;
   my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre');
   while( my $tree = $in->next_tree ) {
   }
 
 

DESCRIPTION

This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees.

Comments

The nexus format allows node comments that are placed inside square brackets. Usually the comments (implemented as tags for nodes) are used to give a name for an internal node or record the bootstap value, but other uses are possible.

The FigTree program by Andrew Rambaut adds various rendering parameters inside comments and flags these comments by starting them with '&!'. The parameters implemented here are 'label' and 'color'.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-open-bio-dot-org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

  Title   : new
  Args    : -header    => boolean  default is true 
                          print/do not print #NEXUS header
            -translate => boolean default is true
                          print/do not print Node Id translation to a number
 
 

next_tree

  Title   : next_tree
  Usage   : my $tree = $treeio->next_tree
  Function: Gets the next tree in the stream
  Returns : Bio::Tree::TreeI
  Args    : none
 
 

write_tree

  Title   : write_tree
  Usage   : $treeio->write_tree($tree);
  Function: Writes a tree onto the stream
  Returns : none
  Args    : Bio::Tree::TreeI
 
 

header

  Title   : header
  Usage   : $obj->header($newval)
  Function: 
  Example : 
  Returns : value of header (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

translate_node

  Title   : translate_node
  Usage   : $obj->translate_node($newval)
  Function: 
  Example : 
  Returns : value of translate_node (a scalar)
  Args    : on set, new value (a scalar or undef, optional)