bc_relative_to_absolute - Convert relative abundances into absolute
bc_relative_to_absolute -input_files my_communities.generic \ -abundance_file my_counts.tsv \ -output_prefix my_results
This script reads files containing biological communities and a file of abundance for these communities. The relative abundance of each member is multiplied by the total abundance for its community to obtain the absolute abundance of this member.
Input files containing the communities to process. All files must have the same format, which can be one of generic (tab-delimited table), qiime, gaas or unifrac. See Bio::Community::IO for more information on these format.
File containing the total abundance for each community. Each line in the file should be tab-separated and have two columns: community name, total abundance.
Path and prefix for the output files. Several output files will be created if the requested output format can only hold a single community. Default: output_prefix.default
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
http://bugzilla.open-bio.org/
Email florent.angly@gmail.com
To install Bio::Community, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Community
CPAN shell
perl -MCPAN -e shell install Bio::Community
For more information on module installation, please visit the detailed CPAN module installation guide.