Florent Angly > Bio-Community-0.001000 > Bio::Community::IO::Driver::generic

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Source   Latest Release: Bio-Community-0.001007

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 2011,2012,2013 by the BioPerl Team bioperl-l@bioperl.org

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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