NAME

bc_measure_alpha - Measure alpha diversity of communities

SYNOPSIS

bc_measure_alpha -input_files   communities.generic      \
                 -alpha_type    chao1                    \
                 -output_prefix community_alpha

DESCRIPTION

This script reads files containing biological communities and calculates their alpha diversity. The output is a tab-delimited file containing the alpha diversity for each community, with the community names in the first column, and their alpha diversity in the second. Note 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

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

The types of alpha diversity metric to calculate:

* Richness metrics: observed, menhinick, margalef, chao1, ace

* Evenness (equitability) metrics: buzas, heip, shannon_e, simpson_e, brillouin_e, hill_e, mcintosh_e, camargo

* Indices metrics: shannon, simpson, simpson_r, brillouin, hill, mcintosh

* Dominance metrics: simpson_d, berger

See Bio::Community::Alpha for details about these metrics. 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 files. 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