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

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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.

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