1Bio::DB::Taxonomy::listU(s3e)r Contributed Perl DocumentaBtiioo:n:DB::Taxonomy::list(3)
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NAME

6       Bio::DB::Taxonomy::list - An implementation of Bio::DB::Taxonomy that
7       accepts lists of words to build a database
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SYNOPSIS

10         use Bio::DB::Taxonomy;
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12         my @names = ('Eukaryota', 'Mammalia', 'Homo', 'Homo sapiens');
13         my @ranks = qw(superkingdom class genus species);
14         my $db = Bio::DB::Taxonomy->new(-source => 'list', -names => \@names,
15                                                           -ranks => \@ranks);
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17         @names = ('Eukaryota', 'Mammalia', 'Mus', 'Mus musculus');
18         $db->add_lineage(-names => \@names, -ranks => \@ranks);
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DESCRIPTION

21       This is an implementation which uses supplied lists of words to create
22       a database from which you can extract Bio::Taxon objects.
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TODO

25       It is possible this module could do something like store the data it
26       builds up to disc. Would that be useful?  At any rate, this is why the
27       module is called 'list' and not 'in_memory' or similar.
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FEEDBACK

30   Mailing Lists
31       User feedback is an integral part of the evolution of this and other
32       Bioperl modules. Send your comments and suggestions preferably to the
33       Bioperl mailing list.  Your participation is much appreciated.
34
35         bioperl-l@bioperl.org                  - General discussion
36         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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38   Support
39       Please direct usage questions or support issues to the mailing list:
40
41       bioperl-l@bioperl.org
42
43       rather than to the module maintainer directly. Many experienced and
44       reponsive experts will be able look at the problem and quickly address
45       it. Please include a thorough description of the problem with code and
46       data examples if at all possible.
47
48   Reporting Bugs
49       Report bugs to the Bioperl bug tracking system to help us keep track of
50       the bugs and their resolution. Bug reports can be submitted via the
51       web:
52
53         http://bugzilla.open-bio.org/
54

AUTHOR - Sendu Bala

56       Email bix@sendu.me.uk
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APPENDIX

59       The rest of the documentation details each of the object methods.
60       Internal methods are usually preceded with a _
61
62   new
63        Title   : new
64        Usage   : my $obj = Bio::DB::Taxonomy::list->new();
65        Function: Builds a new Bio::DB::Taxonomy::list object
66        Returns : an instance of Bio::DB::Taxonomy::list
67        Args    : optional, as per the add_lineage() method.
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69   add_lineage
70        Title   : add_lineage
71        Usage   : $db->add_lineage(-names => \@names)
72        Function: Add a lineage to the database, where the lineage is described by
73                  a list of scientific names in the order root->leaf. The rank of each
74                  name can optionally be described by supplying an additional list
75                  of rank names in the same order (eg. superkingdom->species).
76        Returns : n/a
77        Args    : -names => [] : array ref of scientific names, REQUIRED
78                  -ranks => [] : array ref of rank names, same order as above, OPTIONAL
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80   Bio::DB::Taxonomy Interface implementation
81   get_taxon
82        Title   : get_taxon
83        Usage   : my $taxon = $db->get_taxon(-taxonid => $taxonid)
84        Function: Get a Bio::Taxon object from the database.
85        Returns : Bio::Taxon object
86        Args    : just a single value which is the database id, OR named args:
87                  -taxonid => taxonomy id (to query by taxonid; NB: these are not
88                              NCBI taxonomy ids but 'list' pre-fixed ids unique to the
89                              list database)
90                   OR
91                  -name    => string (to query by a taxonomy name)
92
93   get_taxonids
94        Title   : get_taxonids
95        Usage   : my @taxonids = $db->get_taxonids('Homo sapiens');
96        Function: Searches for a taxonid (generated by the list module) based on a
97                  query string. Note that multiple taxonids can match to the same
98                  supplied name.
99        Returns : array of integer ids in list context, one of these in scalar context
100        Args    : string representing taxon's name
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102   ancestor
103        Title   : ancestor
104        Usage   : my $ancestor_taxon = $db->ancestor($taxon)
105        Function: Retrieve the full ancestor taxon of a supplied Taxon from the
106                  database.
107        Returns : Bio::Taxon
108        Args    : Bio::Taxon (that was retrieved from this database)
109
110   each_Descendent
111        Title   : each_Descendent
112        Usage   : my @taxa = $db->each_Descendent($taxon);
113        Function: Get all the descendents of the supplied Taxon (but not their
114                  descendents, ie. not a recursive fetchall).
115        Returns : Array of Bio::Taxon objects
116        Args    : Bio::Taxon (that was retrieved from this database)
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120perl v5.12.0                      2010-04-29        Bio::DB::Taxonomy::list(3)