| Bio::TreeIO::nexus(3pm) | User Contributed Perl Documentation | Bio::TreeIO::nexus(3pm) |
Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP
use Bio::TreeIO;
my $in = Bio::TreeIO->new(-file => 't/data/cat_tre.tre');
while( my $tree = $in->next_tree ) {
}
This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees.
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 bootstrap 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'.
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
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.
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:
https://github.com/bioperl/bioperl-live/issues
Email jason-at-open-bio-dot-org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none
Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : Bio::Tree::TreeI
Title : header Usage : $obj->header($newval) Function: Example : Returns : value of header (a scalar) Args : on set, new value (a scalar or undef, optional)
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)
| 2018-10-27 | perl v5.26.2 |