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

NAME

Bio::Community::IO::Driver::unifrac - Driver to read and write files in the (Fast)Unifrac format

SYNOPSIS

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

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

DESCRIPTION

This Bio::Community::IO::Driver::unifrac driver reads and writes Unifrac environment files and FastUnifrac sample ID mapping files, whose format is described at http://bmf2.colorado.edu/unifrac/help.psp#env_file and http://bmf2.colorado.edu/fastunifrac/help.psp#sample_id_mapping_file. In this tab-delimited format, the first column is a sequence ID, the second is the name of a community, and the optional third column contains the number of observations of this sequence in the community. Multiple communities can be written in a Unifrac formatted-file and spaces are not supported in community name or member description. Example:

  Sequence.1    Sample.1        1
  Sequence.1    Sample.2        2
  Sequence.2    Sample.1        15
  Sequence.3    Sample.1        2
  Sequence.4    Sample.2        8
  Sequence.5    Sample.1        4
  Sequence.6    Sample.3        1
  Sequence.6    Sample.2        1

For each Bio::Community::Member $member generated from a Unifrac file, $member->desc() contains the content of the first field, i.e. the first column. Since the Unifrac format does not specify a member ID, one is automatically generated and can be retrieved using $member->id().

Note that member counts (the third column) is optional. Example:

  Sequence.1    Sample.1
  Sequence.1    Sample.2
  Sequence.2    Sample.1
  Sequence.3    Sample.1
  Sequence.4    Sample.2
  Sequence.5    Sample.1
  Sequence.6    Sample.3
  Sequence.6    Sample.2

In this case the data is to be interpreted as presence/absence data. When reading a Unifrac file without counts, all members are given a count of 1. Conversely, when writing a Unifrac file, if all members have a count of 1, then the third column is not written. Also, when writing Unifrac files, any spaces in community member name or member description is replaced by a dot.

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.