Enveomics collection

CharTable.classify.rb

Uses a dichotomous key to classify objects parsing a character table.

    See source code, Artistic license 2.0.

§ References

    Rodriguez-R & Konstantinidis, 2016, PeerJ Preprints.

§ Requirements

• Ruby >= 2.0.

§ Usage

CharTable.classify.rb --table in_file --key in_file [opts]

§ Arguments

Table*

 --table in_file  Input table containing the states (columns) per object (row). It must be tab-delimited and with row and column names.

Key*

 --key in_file  Input table containing the dychotomous key in linked style, defined in four columns (can contain #-lead comment lines): (1) ID of the step, typically a sequential integer. (2) Name of character to evaluate. Must coincide with the -t headers. (3) First character decision (see below). (4) Second character decision (see below). A character decision must be formated as: state (must coincide with the values in -t), colon (:), step to follow. If the state is * (star) any state triggers the decision (this should be the norm in column 4). The step to follow should be a step ID in square brackets, or the name of the classification.

Classification

 --classification out_file  Two-column table with the classification of the input objects.

Newick

 --newick out_file  Tree containing all the classified objects. This only makes sense for synoptic keys.

Quiet

 --quiet   Run quietly (no STDERR output).

* Mandatory.