bio::taxonomy::factoryi(3pm) [debian man page]
Bio::Taxonomy::FactoryI(3pm) User Contributed Perl Documentation Bio::Taxonomy::FactoryI(3pm) NAME
Bio::Taxonomy::FactoryI - interface to define how to access NCBI Taxonoy DESCRIPTION
NB: This module has been deprecated. $factory->fetch is a general method to fetch Taxonomy by either NCBI taxid or any types of names. $factory->fetch_parent($taxonomy), returns a Taxonomy that is one-step higher rank of the taxonomy specified as argument. $factory->fetch_children($taxonomy), reports an array of Taxonomy those are one-step lower rank of the taxonomy specified as the argument. AUTHOR - Juguang Xiao juguang@tll.org.sg CONTRIBUTORS
Additional contributors' names and emails here APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ fetch Title: fetch Usage: my $taxonomy = $factory->fetch(-taxon_id => 9605); my $taxonomy = $factory->fetch(-common_name => 'mammals'); Fuctnion: Fetch taxonomy by taxon_id, common name or scientific name. Returns: an instance of Bio::Taxonomy Args: -taxon_id => NCBI taxonomy ID -common_name => comon name, such as 'human', 'mammals' -scientifc_name => specitic name, such as 'sapiens', 'Mammalia' fuzzy_fetch Title: fuzzy_fetch Usage: my @taxonomy = $factory->fuzzy_fetch(-name => 'mouse'); Function: Fuzzy fetch by name, or any text information found in DB Returns: an array reference of Bio::Taxonomy objects Args: -name => any name, such as common name, variant, scientific name -description, or -desc => any text information fetch_parent Title: fetch_parent Usage: my $parent_taxonomy = $factory->fetch_parent($taxonomy); Function: Fetch the parent that is one-rank higher than the argument. Returns: an instance of Bio::Taxonomy, or undef if the arg is the top one. Args: a Bio::Taxonomy object. fetch_children Title: fetch_children Usage: my @children_taxonomy = $factory->fetch_children($taxonomy); Function: Fetch all children those are one-rank lower than the argument. Returns: an array reference of Bio::Taxonomy objects Args: a Bio::Taxonomy object. perl v5.14.2 2012-03-02 Bio::Taxonomy::FactoryI(3pm)
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Bio::Taxon(3pm) User Contributed Perl Documentation Bio::Taxon(3pm) NAME
Bio::Taxon - A node in a represented taxonomy SYNOPSIS
use Bio::Taxon; # Typically you will get a Taxon from a Bio::DB::Taxonomy object # but here is how you initialize one my $taxon = Bio::Taxon->new(-name => $name, -id => $id, -rank => $rank, -division => $div); # Get one from a database my $dbh = Bio::DB::Taxonomy->new(-source => 'flatfile', -directory=> '/tmp', -nodesfile=> '/path/to/nodes.dmp', -namesfile=> '/path/to/names.dmp'); my $human = $dbh->get_taxon(-name => 'Homo sapiens'); $human = $dbh->get_taxon(-taxonid => '9606'); print "id is ", $human->id, " "; # 9606 print "rank is ", $human->rank, " "; # species print "scientific name is ", $human->scientific_name, " "; # Homo sapiens print "division is ", $human->division, " "; # Primates my $mouse = $dbh->get_taxon(-name => 'Mus musculus'); # You can quickly make your own lineages with the list database my @ranks = qw(superkingdom class genus species); my @h_lineage = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens'); my $list_dbh = Bio::DB::Taxonomy->new(-source => 'list', -names => @h_lineage, -ranks => @ranks); $human = $list_dbh->get_taxon(-name => 'Homo sapiens'); my @names = $human->common_names; # @names is empty $human->common_names('woman'); @names = $human->common_names; # @names contains woman # You can switch to another database when you need more information my $entrez_dbh = Bio::DB::Taxonomy->new(-source => 'entrez'); $human->db_handle($entrez_dbh); @names = $human->common_names; # @names contains woman, human, man # Since Bio::Taxon implements Bio::Tree::NodeI, we have access to those # methods (and can manually create our own taxa and taxonomy without the use # of any database) my $homo = $human->ancestor; # Though be careful with each_Descendent - unless you add_Descendent() # yourself, you won't get an answer because unlike for ancestor(), Bio::Taxon # does not ask the database for the answer. You can ask the database yourself # using the same method: ($human) = $homo->db_handle->each_Descendent($homo); # We can also take advantage of Bio::Tree::Tree* methods: # a) some methods are available with just an empty tree object use Bio::Tree::Tree; my $tree_functions = Bio::Tree::Tree->new(); my @lineage = $tree_functions->get_lineage_nodes($human); my $lca = $tree_functions->get_lca($human, $mouse); # b) for other methods, create a tree using your Taxon object my $tree = Bio::Tree::Tree->new(-node => $human); my @taxa = $tree->get_nodes; $homo = $tree->find_node(-rank => 'genus'); # Normally you can't get the lca of a list-database derived Taxon and an # entrez or flatfile-derived one because the two different databases might # have different roots and different numbers of ranks between the root and the # taxa of interest. To solve this, make a tree of the Taxon with the more # detailed lineage and splice out all the taxa that won't be in the lineage of # your other Taxon: my $entrez_mouse = $entrez_dbh->get_taxon(-name => 'Mus musculus'); my $list_human = $list_dbh->get_taxon(-name => 'Homo sapiens'); my $mouse_tree = Bio::Tree::Tree->new(-node => $entrez_mouse); $mouse_tree->splice(-keep_rank => @ranks); $lca = $mouse_tree->get_lca($entrez_mouse, $list_human); DESCRIPTION
This is the next generation (for Bioperl) of representing Taxonomy information. Previously all information was managed by a single object called Bio::Species. This new implementation allows representation of the intermediate nodes not just the species nodes and can relate their connections. 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: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Sendu Bala Email bix@sendu.me.uk CONTRIBUTORS
Jason Stajich, jason-at-bioperl-dot-org (original Bio::Taxonomy::Node) Juguang Xiao, juguang@tll.org.sg Gabriel Valiente, valiente@lsi.upc.edu APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::Taxonomy::Node->new(); Function: Builds a new Bio::Taxonomy::Node object Returns : an instance of Bio::Taxonomy::Node Args : -dbh => a reference to a Bio::DB::Taxonomy object [no default] -name => a string representing the taxon name (scientific name) -id => human readable id - typically NCBI taxid -ncbi_taxid => same as -id, but explicitly say that it is an NCBI taxid -rank => node rank (one of 'species', 'genus', etc) -common_names => array ref of all common names -division => 'Primates', 'Rodents', etc -genetic_code => genetic code table number -mito_genetic_code => mitochondrial genetic code table number -create_date => date created in database -update_date => date last updated in database -pub_date => date published in database Bio::IdentifiableI interface Also see Bio::IdentifiableI version Title : version Usage : $taxon->version($newval) Returns : value of version (a scalar) Args : on set, new value (a scalar or undef, optional) authority Title : authority Usage : $taxon->authority($newval) Returns : value of authority (a scalar) Args : on set, new value (a scalar or undef, optional) namespace Title : namespace Usage : $taxon->namespace($newval) Returns : value of namespace (a scalar) Args : on set, new value (a scalar or undef, optional) Bio::Taxonomy::Node implementation db_handle Title : db_handle Usage : $taxon->db_handle($newval) Function: Get/Set Bio::DB::Taxonomy Handle Returns : value of db_handle (a scalar) (Bio::DB::Taxonomy object) Args : on set, new value (a scalar, optional) Bio::DB::Taxonomy object Also see Bio::DB::Taxonomy rank Title : rank Usage : $taxon->rank($newval) Function: Get/set rank of this Taxon, 'species', 'genus', 'order', etc... Returns : value of rank (a scalar) Args : on set, new value (a scalar or undef, optional) id Title : id Usage : $taxon->id($newval) Function: Get/Set id (NCBI Taxonomy ID in most cases); object_id() and ncbi_taxid() are synonyms of this method. Returns : id (a scalar) Args : none to get, OR scalar to set ncbi_taxid Title : ncbi_taxid Usage : $taxon->ncbi_taxid($newval) Function: Get/Set the NCBI Taxonomy ID; This actually sets the id() but only returns an id when ncbi_taxid has been explictely set with this method. Returns : id (a scalar) Args : none to get, OR scalar to set parent_id Title : parent_id Usage : $taxon->parent_id() Function: Get parent ID, (NCBI Taxonomy ID in most cases); parent_taxon_id() is a synonym of this method. Returns : value of parent_id (a scalar) Args : none Status : deprecated genetic_code Title : genetic_code Usage : $taxon->genetic_code($newval) Function: Get/set genetic code table Returns : value of genetic_code (a scalar) Args : on set, new value (a scalar or undef, optional) mitochondrial_genetic_code Title : mitochondrial_genetic_code Usage : $taxon->mitochondrial_genetic_code($newval) Function: Get/set mitochondrial genetic code table Returns : value of mitochondrial_genetic_code (a scalar) Args : on set, new value (a scalar or undef, optional) create_date Title : create_date Usage : $taxon->create_date($newval) Function: Get/Set Date this node was created (in the database) Returns : value of create_date (a scalar) Args : on set, new value (a scalar or undef, optional) update_date Title : update_date Usage : $taxon->update_date($newval) Function: Get/Set Date this node was updated (in the database) Returns : value of update_date (a scalar) Args : on set, new value (a scalar or undef, optional) pub_date Title : pub_date Usage : $taxon->pub_date($newval) Function: Get/Set Date this node was published (in the database) Returns : value of pub_date (a scalar) Args : on set, new value (a scalar or undef, optional) ancestor Title : ancestor Usage : my $ancestor_taxon = $taxon->ancestor() Function: Retrieve the ancestor taxon. Normally the database is asked what the ancestor is. If you manually set the ancestor (or you make a Bio::Tree::Tree with this object as an argument to new()), the database (if any) will not be used for the purposes of this method. To restore normal database behaviour, call ancestor(undef) (which would remove this object from the tree), or request this taxon again as a new Taxon object from the database. Returns : Bio::Taxon Args : none get_Parent_Node Title : get_Parent_Node Function: Synonym of ancestor() Status : deprecated each_Descendent Title : each_Descendent Usage : my @taxa = $taxon->each_Descendent(); Function: Get all the descendents for this Taxon (but not their descendents, ie. not a recursive fetchall). get_Children_Nodes() is a synonym of this method. Note that this method never asks the database for the descendents; it will only return objects you have manually set with add_Descendent(), or where this was done for you by making a Bio::Tree::Tree with this object as an argument to new(). To get the database descendents use $taxon->db_handle->each_Descendent($taxon). Returns : Array of Bio::Taxon objects Args : optionally, when you have set your own descendents, the string "height", "creation", "alpha", "revalpha", or coderef to be used to sort the order of children nodes. get_Children_Nodes Title : get_Children_Nodes Function: Synonym of each_Descendent() Status : deprecated name Title: name Usage: $taxon->name('scientific', 'Homo sapiens'); $taxon->name('common', 'human', 'man'); my @names = @{$taxon->name('common')}; Function: Get/set the names. node_name(), scientific_name() and common_names() are shorthands to name('scientific'), name('scientific') and name('common') respectively. Returns: names (a array reference) Args: Arg1 => the name_class. You can assign any text, but the words 'scientific' and 'common' have the special meaning, as scientific name and common name, respectively. 'scientific' and 'division' are treated specially, allowing only the first value in the Arg2 list to be set. Arg2 .. => list of names node_name Title : node_name Usage : $taxon->node_name($newval) Function: Get/set the name of this taxon (node), typically the scientific name of the taxon, eg. 'Primate' or 'Homo'; scientific_name() is a synonym of this method. Returns : value of node_name (a scalar) Args : on set, new value (a scalar or undef, optional) common_names Title : common_names Usage : $taxon->common_names($newval) Function: Get/add the other names of this taxon, typically the genbank common name and others, eg. 'Human' and 'man'. common_name() is a synonym of this method. Returns : array of names in list context, one of those names in scalar context Args : on add, new list of names (scalars, optional) division Title : division Usage : $taxon->division($newval) Function: Get/set the division this taxon belongs to, eg. 'Primates' or 'Bacteria'. Returns : value of division (a scalar) Args : on set, new value (a scalar or undef, optional) remove_Descendent Title : remove_Descendent Usage : $node->remove_Descedent($node_foo); Function: Removes a specific node from being a Descendent of this node Returns : nothing Args : An array of Bio::Node::NodeI objects which have been previously passed to the add_Descendent call of this object. perl v5.14.2 2012-03-02 Bio::Taxon(3pm)