4.1.8. informative_traits.py

Report information about the traits that are informative, i.e. the traits that don’t have the same value in all species.

The result is a key-value association, either displayed in the console or written to a file as TSV or JSON.

The information reported is:

• The total number of values (keyed TotalSize).
• The number of informative values (keyed InformativesSize).
• The percentage of informative values (keyed PercentageInformative).
• The first non informative value seen during the computation (keyed NonInformativeValue); this was used mainly for debugging.

created:September 2018 last modified:August 2019

4.1.8.1. Usage

Report information about the traits that are informative

usage: informative_traits.py [-h] [-o OUTPUT]
                             [-m {intersection,atLeastTwo,union}] [-p] [-v]
                             orthos values [values ...]

4.1.8.1.1. Positional Arguments

orthos	all the orthos, in TSV
values	the values files, in (Gzipped) TSV

4.1.8.1.2. Named Arguments

-o, --output	write the output there; can be JSON or TSV
-m, --mode	Possible choices: intersection, atLeastTwo, union the mode, that is, the kind of values we want to keep while computing the distance Default: “intersection”
-p, --progress	print a progress bar; need tqdm to be installed Default: False
-v, --verbose	be verbose Default: False