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 = new Bio::DB::Taxonomy(-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
32       User feedback is an integral part of the evolution of this and other
33       Bioperl modules. Send your comments and suggestions preferably to the
34       Bioperl mailing list.  Your participation is much appreciated.
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36         bioperl-l@bioperl.org                  - General discussion
37         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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39       Reporting Bugs
40
41       Report bugs to the Bioperl bug tracking system to help us keep track of
42       the bugs and their resolution. Bug reports can be submitted via the
43       web:
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45         http://bugzilla.open-bio.org/
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AUTHOR - Sendu Bala

48       Email bix@sendu.me.uk
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APPENDIX

51       The rest of the documentation details each of the object methods.
52       Internal methods are usually preceded with a _
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54       new
55
56        Title   : new
57        Usage   : my $obj = new Bio::DB::Taxonomy::list();
58        Function: Builds a new Bio::DB::Taxonomy::list object
59        Returns : an instance of Bio::DB::Taxonomy::list
60        Args    : optional, as per the add_lineage() method.
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62       add_lineage
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64        Title   : add_lineage
65        Usage   : $db->add_lineage(-names => \@names)
66        Function: Add a lineage to the database, where the lineage is described by
67                  a list of scientific names in the order root->leaf. The rank of each
68                  name can optionally be described by supplying an additional list
69                  of rank names in the same order (eg. superkingdom->species).
70        Returns : n/a
71        Args    : -names => [] : array ref of scientific names, REQUIRED
72                  -ranks => [] : array ref of rank names, same order as above, OPTIONAL
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74       Bio::DB::Taxonomy Interface implementation
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76       get_taxon
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78        Title   : get_taxon
79        Usage   : my $taxon = $db->get_taxon(-taxonid => $taxonid)
80        Function: Get a Bio::Taxon object from the database.
81        Returns : Bio::Taxon object
82        Args    : just a single value which is the database id, OR named args:
83                  -taxonid => taxonomy id (to query by taxonid; NB: these are not
84                              NCBI taxonomy ids but 'list' pre-fixed ids unique to the
85                              list database)
86                   OR
87                  -name    => string (to query by a taxonomy name)
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89       get_taxonids
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91        Title   : get_taxonids
92        Usage   : my @taxonids = $db->get_taxonids('Homo sapiens');
93        Function: Searches for a taxonid (generated by the list module) based on a
94                  query string. Note that multiple taxonids can match to the same
95                  supplied name.
96        Returns : array of integer ids in list context, one of these in scalar context
97        Args    : string representing taxon's name
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99       ancestor
100
101        Title   : ancestor
102        Usage   : my $ancestor_taxon = $db->ancestor($taxon)
103        Function: Retrieve the full ancestor taxon of a supplied Taxon from the
104                  database.
105        Returns : Bio::Taxon
106        Args    : Bio::Taxon (that was retrieved from this database)
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108       each_Descendent
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110        Title   : each_Descendent
111        Usage   : my @taxa = $db->each_Descendent($taxon);
112        Function: Get all the descendents of the supplied Taxon (but not their
113                  descendents, ie. not a recursive fetchall).
114        Returns : Array of Bio::Taxon objects
115        Args    : Bio::Taxon (that was retrieved from this database)
116
117       Helper methods
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119perl v5.8.8                       2007-05-07        Bio::DB::Taxonomy::list(3)
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