Florent Angly > Bio-Community-0.001000 > Bio::Community::Tools::RepresentativeIdConverter

Download:
Bio-Community-0.001000.tar.gz

Dependencies

Annotate this POD

Website

View/Report Bugs
Source   Latest Release: Bio-Community-0.001004

NAME ^

Bio::Community::Tools::RepresentativeIdConverter - Convert member ID to OTU representative ID or taxonomic ID

SYNOPSIS ^

  use Bio::Community::Tools::RepresentativeIdConverter;

  my $converter = Bio::Community::Tools::Summarizer->new(
     -metacommunity => $meta,
     -cluster_file  => 'gg_99_otu_map.txt',
  );
  my $meta_by_otu = $converter->get_converted_meta;

DESCRIPTION ^

Given a metacommunity and an OTU cluster map file (or taxonomic assignment file), replace the ID of every member by that of its OTU cluster (or taxonomic) representative and add it in a new metacommunity.

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 _

new

 Function: Create a new Bio::Community::Tool::RepresentativeIdConverter object
 Usage   : my $converter = Bio::Community::Tool::RepresentativeIdConverter->new(
              -metacommunity => $meta,
              -cluster_file  => '99_otu_map.txt',
           );
           # or
           my $converter = Bio::Community::Tool::RepresentativeIdConverter->new(
              -metacommunity  => $meta,
              -taxassign_file => 'rep_set_tax_assignments.txt',
           );
 Args    : -metacommunity  : See metacommunity().
           -cluster_file   : See cluster_file().
           -taxassign_file : See taxassign_file().
           Use either -cluster_file or -taxassign_file
 Returns : a Bio::Community::Tools::RepresentativeIdConverter object

metacommunity

 Function: Get/set communities, given as metacommunity, to summarize.
 Usage   : my $meta = $summarizer->metacommunity;
 Args    : A Bio::Community::Meta object
 Returns : A Bio::Community::Meta object

cluster_file

 Function: Get / set the tab-delimited file that defines the OTU clusters. The
           columns are: OTU ID, ID of the representative sequence, IDs of the
           other sequences in the OTU. For example:

               0        367523
               1        187144
               2        544886  544649
               3        310669
               4        355095  310677  347705  563209

           The OTU files distributed by Greengenes use this format (e.g.,
           99_otu_map.txt).
 Usage   : $summarizer->cluster_file('99_otu_map.txt');
 Args    : OTU cluster file name
 Returns : OTU cluster file name

taxassign_file

 Function: Get / set the tab-delimited file that defines the OTU taxonomic
           assignemts. The first four columns (out of 12) should be: OTU ID,
           taxonomic string, E-value, taxonomic ID. For example:

           345     k__Bacteria; p__Actinobacteria; c__Actinobacteria; o__Actinomycetales; f__Propionibacteriaceae; g__Propionibacterium; s__acnes  5e-138  1042485 95.67   300     13      0       1       300     878     579
           346     k__Bacteria; p__Firmicutes; c__Bacilli; o__; f__; g__; s__      8e-134  1064834 99.59   245     1       0       1       245     909     665
           347     k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Pseudomonadales; f__Pseudomonadaceae; g__Pseudomonas; s__    2e-103  959954  98.99   198     2       0       103     300     718     521

           The taxonomic assignment files generated by QIIME (rep_set_tax_assignments.txt)
           follow this format.
 Usage   : $summarizer->taxassign_file('rep_set_tax_assignments.txt');
 Args    : taxonomic assignment file name
 Returns : taxonomic assignment file name

get_converted_meta

 Function: Convert the communities and return the corresponding metacommunity.
 Usage   : my $meta_by_otu = $converter->get_converted_meta;
 Args    : None
 Returns : A Bio::Community::Meta object
syntax highlighting: