Bio::Community::IO::Driver::qiime - Driver to read and write files in the QIIME format
my $in = Bio::Community::IO->new( -file => 'qiime_communities.txt', -format => 'qiime' ); # See Bio::Community::IO for more information
This Bio::Community::IO::Driver::qiime driver reads and writes files generated by QIIME (http://qiime.org/). Multiple communities can be recorded in a tab-delimited file. Here is an example of QIIME OTU table file:
# QIIME v1.3.0 OTU table #OTU ID soil marine freshwater 0 3 11 0 1 10 24 0 2 0 230 110 3 0 30 80
Note that the first line is an arbitrary comment line, which can be used to specify a metacommunity name. The second line contains column names. Here is the same OTU table with a given metacommunity name (the first line) and assignments to the GreenGenes taxonomy:
# biome_comparison_2013 #OTU ID soil marine freshwater Consensus Lineage 0 3 11 0 k__Bacteria;p__Cyanobacteria;c__;o__Chroococcales;f__;g__Synechococcus;s__ 1 10 24 0 k__Bacteria;p__TM6;c__;o__;f__;g__;s__ 2 0 230 110 k__Bacteria;p__Cyanobacteria;c__;o__Oscillatoriales;f__;g__Trichodesmium;s__Trichodesmium erythraeum 3 0 30 80 k__Bacteria;p__Acidobacteria;c__Solibacteres;o__Solibacterales;f__Solibacteraceae;g__Candidatus Solibacter;s__
To be recognized, the last column must match the pattern *lineage* or *taxon*.
For each Bio::Community::Member $member generated from a QIIME file, $member->id() contains the OTU ID, while $member->desc() holds the content of the consensus lineage field.
Note: QIIME also provides OTU tables summarized at the different taxonomic levels, with relative abundance instead of counts:
Taxon soil marine freshwater k__Bacteria;p__Acidobacteria 0.0 0.1016949153 0.4210526316 k__Bacteria;p__Cyanobacteria 0.2307692308 0.8169491525 0.5789473684 k__Bacteria;p__TM6 0.7692307692 0.0813559322 0.0
These tables have to be read and written using the Bio::Community::IO::Driver::generic module, not with Bio::Community::IO::Driver::qiime.
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 2011-2014 by Florent Angly <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.