Bio::Community::Tools::RepresentativeIdConverter - Convert member ID to OTU representative ID or taxonomic ID
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;
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.
Florent Angly firstname.lastname@example.org
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, email@example.com, 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 2011,2012,2013 by the BioPerl Team firstname.lastname@example.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.
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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
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
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