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Bio-Community-0.001008
River stage zero No dependents
1 ++
/ Bio::Community::IO::Driver::qiime

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.