Florent Angly
and 1 contributors

NAME

Bio::Community::IO::Driver::generic - Driver to read and write files in a generic tab-delimited site-by-species table format

SYNOPSIS

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

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

DESCRIPTION

This Bio::Community::IO::Driver::generic driver reads and writes files in a generic format. Multiple communities can be written in a file to generate a site-by- species table (OTU table), in which the entries are tab-delimited. Example:

  Species       site A  site B
  species 1     321     94
  species 2     0       58
  species 3     47      26

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

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.