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

NAME

Bio::Community::IO::Driver::gaas - Driver to read and write files in the GAAS format

SYNOPSIS

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

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

DESCRIPTION

This Bio::Community::IO::Driver::gaas driver reads and writes files in the format generated by GAAS (http://sourceforge.net/projects/gaas/). GAAS creates one such file per community. Here is an example:

  # tax_name    tax_id  rel_abund
  Streptococcus pyogenes phage 315.1    198538  0.791035649011735
  Goatpox virus Pellor  376852  0.196094208626593
  Lumpy skin disease virus NI-2490      376849  0.0128701423616715

For each Bio::Community::Member $member generated from a GAAS file, $member->id() contains the content of the tax_id field, while $member->desc() reflects the tax_name field.

Note that GAAS format does not include counts for the community members but relative abundances only. Thus, the get_members_count() method of the Bio::Community objects generated using this driver is a relative abundance (a decimal number) instead of the usual integers used for counts.

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.