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Bio::Tree::TreeFunctionsI.3pm
Langue: en
Version: 2008-06-24 (ubuntu - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methodsSYNOPSIS
use Bio::TreeIO; my $in = new Bio::TreeIO(-format => 'newick', -file => 'tree.tre'); my $tree = $in->next_tree; my @nodes = $tree->find_node('id1'); if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outnode) ){ #... }
DESCRIPTION
This interface provides a set of implementated Tree functions which only use the defined methods in the TreeI or NodeI interface.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
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, Aaron Mackey, Justin Reese
Email jason-at-bioperl-dot-org Email amackey-at-virginia.edu Email jtr4v-at-virginia.eduCONTRIBUTORS
Sendu Bala, bix@sendu.me.ukRerooting code was worked on by
Daniel Barker d.barker-at-reading.ac.uk Ramiro Barrantes Ramiro.Barrantes-at-uvm.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _find_node
Title : find_node Usage : my @nodes = $self->find_node(-id => 'node1'); Function: returns all nodes that match a specific field, by default this is id, but different branch_length, Returns : List of nodes which matched search Args : text string to search for OR -fieldname => $textstring
remove_Node
Title : remove_Node Usage : $tree->remove_Node($node) Function: Removes a node from the tree Returns : boolean represent status of success Args : either Bio::Tree::NodeI or string of the node id
get_lineage_nodes
Title : get_lineage_nodes Usage : my @nodes = $tree->get_lineage_nodes($node); Function: Get the full lineage of a node (all its ancestors, in the order root->most recent ancestor) Returns : list of nodes Args : either Bio::Tree::NodeI or string of the node id
splice
Title : splice Usage : $tree->splice(-remove_id => \@ids); Function: Remove all the nodes from a tree that correspond to the supplied args, making all the descendents of a removed node the descendents of the removed node's ancestor. You can ask to explicitly remove certain nodes by using -remove_*, remove them conditionally by using -remove_* in combination with -keep_*, or remove everything except certain nodes by using only -keep_*. Returns : n/a Args : just a list of Bio::Tree::NodeI objects to remove, OR -key => value pairs, where -key has the prefix 'remove' or 'keep', followed by an underscore, followed by a fieldname (like for the method find_node). Value should be a scalar or an array ref of scalars (again, like you might supply to find_node). So (-remove_id => [1, 2]) will remove all nodes from the tree that have an id() of '1' or '2', while (-remove_id => [1, 2], -keep_id => [2]) will remove all nodes with an id() of '1'. (-keep_id => [2]) will remove all nodes unless they have an id() of '2' (note, no -remove_*).
get_lca
Title : get_lca Usage : get_lca(-nodes => \@nodes ); OR get_lca(@nodes); Function: given two or more nodes, returns the lowest common ancestor (aka most recent common ancestor) Returns : node object or undef if there is no commen ancestor Args : -nodes => arrayref of nodes to test, OR just a list of nodes
merge_lineage
Title : merge_lineage Usage : merge_lineage($node) Function: Merge a lineage of nodes with this tree. Returns : n/a Args : Bio::Tree::TreeI with only one leaf, OR Bio::Tree::NodeI which has an ancestor For example, if we are the tree $tree: +---B | A | +---C and we want to merge the lineage $other_tree: A---C---D After calling $tree->merge_lineage($other_tree), $tree looks like: +---B | A | +---C---D
contract_linear_paths
Title : contract_linear_paths Usage : contract_linear_paths() Function: Splices out all nodes in the tree that have an ancestor and only one descendent. Returns : n/a Args : none For example, if we are the tree $tree: +---E | A---B---C---D | +---F After calling $tree->contract_linear_paths(), $tree looks like: +---E | A---D | +---F
distance
Title : distance Usage : distance(-nodes => \@nodes ) Function: returns the distance between two given nodes Returns : numerical distance Args : -nodes => arrayref of nodes to test
is_monophyletic
Title : is_monophyletic Usage : if( $tree->is_monophyletic(-nodes => \@nodes, -outgroup => $outgroup) Function: Will do a test of monophyly for the nodes specified in comparison to a chosen outgroup Returns : boolean Args : -nodes => arrayref of nodes to test -outgroup => outgroup to serve as a reference
is_paraphyletic
Title : is_paraphyletic Usage : if( $tree->is_paraphyletic(-nodes =>\@nodes, -outgroup => $node) ){ } Function: Tests whether or not a given set of nodes are paraphyletic (representing the full clade) given an outgroup Returns : [-1,0,1] , -1 if the group is not monophyletic 0 if the group is not paraphyletic 1 if the group is paraphyletic Args : -nodes => Array of Bio::Tree::NodeI objects which are in the tree -outgroup => a Bio::Tree::NodeI to compare the nodes to
reroot
Title : reroot Usage : $tree->reroot($node); Function: Reroots a tree making a new node the root Returns : 1 on success, 0 on failure Args : Bio::Tree::NodeI that is in the tree, but is not the current root
findnode_by_id
Title : findnode_by_id Usage : my $node = $tree->find_node_by_id($id); Function: Get a node by its internal id (which should be unique for the tree) Returns : L<Bio::Tree::NodeI> Args : node id
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