| Bio::TreeIO(3pm) | User Contributed Perl Documentation | Bio::TreeIO(3pm) |
Bio::TreeIO - Parser for Tree files
{
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'newick',
-file => 'globin.dnd');
while( my $tree = $treeio->next_tree ) {
print "Tree is ", $tree->number_nodes, "\n";
}
}
This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI objects.
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-bioperl-dot-org
Allen Day <allenday@ucla.edu>
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new
Usage : my $obj = Bio::TreeIO->new();
Function: Builds a new Bio::TreeIO object
Returns : Bio::TreeIO
Args : a hash. useful keys:
-format : Specify the format of the file. Supported formats:
newick Newick tree format
nexus Nexus tree format
nhx NHX tree format
svggraph SVG graphical representation of tree
tabtree ASCII text representation of tree
lintree lintree output format
Title : format Usage : $format = $obj->format() Function: Get the tree format Returns : tree format Args : none
Title : next_tree Usage : my $tree = $treeio->next_tree; Function: Gets the next tree off the stream Returns : Bio::Tree::TreeI or undef if no more trees Args : none
Title : write_tree Usage : $treeio->write_tree($tree); Function: Writes a tree onto the stream Returns : none Args : Bio::Tree::TreeI
Title : attach_EventHandler Usage : $parser->attatch_EventHandler($handler) Function: Adds an event handler to listen for events Returns : none Args : Bio::Event::EventHandlerI
Title : _eventHandler Usage : private Function: Get the EventHandler Returns : Bio::Event::EventHandlerI Args : none
Title : _load_format_module Usage : *INTERNAL TreeIO stuff* Function: Loads up (like use) a module at run time on demand Example : Returns : Args :
Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args :
| 2020-10-28 | perl v5.30.3 |