Florent Angly > Bio-Community > Bio::Community::IO::Driver::qiime

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NAME ^

Bio::Community::IO::Driver::qiime - Driver to read and write files in the QIIME format

SYNOPSIS ^

   my $in = Bio::Community::IO->new( -file => 'qiime_communities.txt', -format => 'qiime' );

   # See Bio::Community::IO for more information

DESCRIPTION ^

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.

CONSTRUCTOR ^

See Bio::Community::IO.

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 2011-2014 by Florent Angly <florent.angly@gmail.com>

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.

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