NAME

bc_rarefy - Rarefy communities

SYNOPSIS

bc_rarefy -input_files   my_communities.generic   \
          -output_prefix my_converted_communities \
          -sample_size   1000

DESCRIPTION

This script reads a file containing biological communities and performs rarefaction, i.e. repeatedly takes a random subset of the community members, in order to normalize communities by member count. Rarefaction is useful to simulate an identical sampling effort for all communities. The output is a file containing rarefied, representative communities (integers). See Bio::Community::Tools::Rarefier for more information.

REQUIRED ARGUMENTS

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

Input file containing the communities to rarefy. When providing communities in a format that supports only one community per file (e.g. gaas), you can provide multiple input files.

OPTIONAL ARGUMENTS

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output files. Default: output_prefix.default

-ss <sample_size> | -sample_size <sample_size>

Number of members to randomly take at each bootstrap iteration. If omitted, the sample size defaults to the size (member count) of the smallest community.

-dt <dist_threshold> | -dist_threshold <dist_threshold>

Keep doing bootstrap iterations until the distance between the current average community and the average community at the previous iteration becomes less than the specified threshold. Default: dist_threshold.default

-nr <num_repetitions> | -num_repetitions <num_repetitions>

Perform the specified number of bootstrap iterations instead of a dynamic number of iterations based on a distance threshold. As a special case, use 'inf' to assume an infinite number of repetitions.

-wa <write_average> | -write_average <write_average>

Write the average bootstraped communities (decimals) in addition to the rarefied communities (integers): 1 is yes, 0 is no. Default: write_average.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