Florent Angly > Bio-Community > bc_relative_to_absolute

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NAME ^

bc_relative_to_absolute - Convert relative abundances into absolute

SYNOPSIS ^

  bc_relative_to_absolute -input_files     my_communities.generic \
                          -abundance_file  my_counts.tsv          \
                          -output_prefix   my_results

DESCRIPTION ^

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.

REQUIRED ARGUMENTS ^

-if <input_files>... | -input_files <input_files>...

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.

-af <abundance_file> | -abundance_file <abundance_file>

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.

OPTIONAL ARGUMENTS ^

-op <output_prefix> | -output_prefix <output_prefix>

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

FEEDBACK ^

Mailing Lists

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

Support

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.

Reporting Bugs

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/

AUTHOR - Florent Angly ^

Email florent.angly@gmail.com

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