NAME

bc_accumulate - Create species accumulation curves (collector or rarefaction)

SYNOPSIS

bc_accumulate -input_files     communities.generic      \
              -type            collector                \
              -num_repetitions 20                       \
              -alpha_type      menhinick                \
              -output_prefix   community_alpha

DESCRIPTION

This script reads files containing biological communities generates an accumulation curve, either collector or rarefaction.

In a rarefaction curve, an increasing number of randomly drawn members is sampled from the given communities and alpha diversity is calculated. In a collector curve, an increasing number of communities is randomly drawn and combined and their cumulative alpha diversity is determined.

The output is a tab-delimited file containing the average alpha diversity at each sampling depth, with the community names in the first row. Note that no plot is actually drawn. Note also that some alpha diversity metrics are based on relative abundances, and may thus be affected by the weights you provide.

REQUIRED ARGUMENTS

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

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

OPTIONAL ARGUMENTS

-t <type> | -type <type>

The types of species accumulation curve to produce, either 'rarefaction' or 'collector'. Default: type.default

-nr <num_repetitions> | -num_repetitions <num_repetitions>

The number of repetitions to perform at each sampling depth. Default: num_repetitions.default

-nt <num_ticks> | -num_ticks <num_ticks>

For rarefaction curves, specify how many different numbers of individuals to sample, for the smallest community. This number may not always be honored because ticks have to be integers. Default: num_ticks.default

-ts <tick_spacing> | -tick_spacing <tick_spacing>

The type of spacing between the ticks of a rarefaction curve, either linear or logarithmic. Default: tick_spacing.default

-at <alpha_types>... | -alpha_types <alpha_types>...

The types of alpha diversity metric to calculate at each repetition. See Bio::Community::Alpha for the complete list of metrics available. Default: alpha_types.default

-wf <weight_files>... | -weight_files <weight_files>...

Tab-delimited files containing weights to assign to the community members.

-wa <weight_assign> | -weight_assign <weight_assign>

When using a files of weights, define what to do for community members whose weight is not specified in the weight file (default: weight_assign.default):

* $num : assign to the member the arbitrary weight $num provided

* average : assign to the member the average weight in this file.

* ancestor: go up the taxonomic lineage of the member and assign to it the weight of the first ancestor that has a weight in the weights file. Fall back to the 'average' method if no taxonomic information is available for this member (for example a member with no BLAST hit).

-op <output_prefix> | -output_prefix <output_prefix>

Path and prefix for the output file. 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 responsive 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