Bio::TreeIO - Parser for Tree files
{ use Bio::TreeIO; my $treeio = new Bio::TreeIO('-format' => 'newick', '-file' => 'globin.dnd'); while( my $tree = $treeio->next_tree ) { print "Tree is ", $tree->size, "\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.
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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 = new Bio::TreeIO(); 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 : 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 : newline_each_node Usage : $obj->newline_each_node($newval) Function: Get/set newline each node flag which is only applicable for writing tree formats for nhx and newick, will print a newline after each node or paren Returns : value of newline_each_node (boolean) Args : on set, new value (a boolean or undef, optional)
Title : _guess_format Usage : $obj->_guess_format($filename) Function: Example : Returns : guessed format of filename (lower case) Args :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.