bc_rarefy - Rarefy communities
bc_rarefy -input_files my_communities.generic \ -output_prefix my_converted_communities \ -sample_size 1000
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.
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.
Path and prefix for the output files. Default: output_prefix.default
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.
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
Perform the specified number of bootstrap iterations instead of a dynamic number of iterations based on a distance threshold.
Write the average bootstraped communities (decimals) in addition to the rarefied communities (integers): 1 is yes, 0 is no. Default: write_average.default
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Your participation is much appreciated.
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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.
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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.