Florent Angly > Bio-Community-0.001005 > Bio::Community::IO::Driver::biom



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Bio::Community::IO::Driver::biom - Driver to read and write files in the sparse BIOM format


   # Reading
   my $in = Bio::Community::IO->new(
      -file   => 'biom_communities.txt',
      -format => 'biom'
   my $type = $in->get_matrix_type; # either dense or sparse

   # Writing
   my $out = Bio::Community::IO->new(
      -file        => 'biom_communities.txt',
      -format      => 'biom',
      -matrix_type => 'sparse', # default matrix type

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


This Bio::Community::IO::Driver::biom driver reads and writes files in the BIOM format version 1.0 described at http://biom-format.org/documentation/format_versions/biom-1.0.html. Multiple communities and additional metadata can be recorded in a BIOM file. Here is an example of minimal sparse BIOM file:

      "format": "Biological Observation Matrix 0.9.1-dev",
      "format_url": "http://biom-format.org",
      "type": "OTU table",
       "generated_by": "QIIME revision 1.4.0-dev",
      "date": "2011-12-19T19:00:00",
              {"id":"GG_OTU_1", "metadata":null},
              {"id":"GG_OTU_2", "metadata":null},
              {"id":"GG_OTU_3", "metadata":null},
              {"id":"GG_OTU_4", "metadata":null},
              {"id":"GG_OTU_5", "metadata":null}
      "columns": [
              {"id":"Sample1", "metadata":null},
              {"id":"Sample2", "metadata":null},
              {"id":"Sample3", "metadata":null},
              {"id":"Sample4", "metadata":null},
              {"id":"Sample5", "metadata":null},
              {"id":"Sample6", "metadata":null}
      "matrix_type": "sparse",
      "matrix_element_type": "int",
      "shape": [5, 6],

Columns (i.e. communities) can be expressed in a richer way, e.g.:

  {"id":"Sample1", "metadata":{
                           "Description":"human gut"}},

The 'id' can be recovered from the name() method of the resulting Bio::Community. Metadata fields are not recorded at this time, but will be in a future release.

Rows (i.e. community members) can also be expressed in a richer form:

  {"id":"GG_OTU_1", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}},

For each Bio::Community::Member generated, the id() method contains the 'id' and desc() holds a concatenated version of the 'taxonomy' field. Note that you can omit members entirely from a biom file and simply have community names and metadata.

The 'comment' field of biom files is not recorded and simply ignored.


See Bio::Community::IO.


Florent Angly florent.angly@gmail.com


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 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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