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Florent Angly > Bio-Community-0.001005 > bc_rarefy


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Source   Latest Release: Bio-Community-0.001007


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.


-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.


-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


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AUTHOR - Florent Angly ^


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