NAME

Bio::Community::TaxonomyUtils - Functions for manipulating taxonomic lineages

SYNOPSIS

  use Bio::Community::TaxonomyUtils qw(split_lineage_string get_lineage_string);

  my $lineage = 'Bacteria;WCHB1-60;unidentified';
  my $lineage_arr = split_lineage_string($lineage);
  $lineage = get_lineage_string($lineage_arr);

  print "Lineage is: $lineage\n"; # Bacteria;WCHB1-60

DESCRIPTION

This module implements functions to manipulate taxonomic lineages, as arrayref of taxon names or taxon objects.

AUTHOR

Florent Angly florent.angly@gmail.com

SUPPORT AND BUGS

User feedback is an integral part of the evolution of this and other Bioperl modules. 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.

If you have found a bug, please report it on the BioPerl bug tracking system to help us keep track the bugs and their resolution: https://redmine.open-bio.org/projects/bioperl/

COPYRIGHT

Copyright 2011,2012,2013 by the BioPerl Team bioperl-l@bioperl.org

This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself, either Perl version 5.10.1 or, at your option, any later version of Perl 5 you may have available.

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

split_lineage_string

 Function: Split a lineage string, clean it and autodetect whitespaces.
           Use the ';' separator is used to split lineages like 'Bacteria;
           Proteobacteria' into an arrayref of its individual components, e.g.
           ['Bacteria','Proteobact']. The number and type of spaces after the
           separator is saved for future use in get_lineage_string(), the
           reciprocal function. Also, optionally clean the arrayref using
           clean_lineage_arr().
 Usage   : my $taxa_names = split_lineage($lineage_string);
 Args    : * a lineage string
           * whether to clean taxonomy or not (default is to clean)
 Returns : an arrayref of taxon names

clean_lineage_arr

 Function: Two step cleanup:
           1/ At the beginning of the array, remove anything called 'Root'
           2/ Starting from the end of the array, remove ambiguous taxonomic
              information such as:
                '', 'No blast hit', 'unidentified', 'uncultured', 'environmental',
                'Other', 'g__', 's__', etc
 Usage   : $lineage_arr = clean_lineage_arr($lineage_arr);
 Args    : A lineage arrayref (either taxon names or objects)
 Returns : A lineage arrayref

get_taxon_lineage

 Function: Take a taxon object and return its lineage as an arrayref of the
           taxon itself, preceded by its ancestor taxa.
 Usage   : my $lineage_arr = get_taxon_lineage($taxon);
 Args    : A taxon object
 Returns : An arrayref of taxon names

get_lineage_string

 Function: Take a lineage arrayref and return a full lineage string by joining
           the elements using the ';' separator. The opposite operation is
           split_lineage_string().
 Usage   : my $lineage = get_lineage_string(['Bacteria', 'Proteobacteria']);
             or
           my $lineage = get_lineage_string([$taxon1, $taxon2]);
 Args    : * Arrayref of taxon names or objects
           * Optional: whitespace string to include after separator (omit to autodetect)
 Returns : A lineage string