1. Author Information

Author: benben-miao

Email: benben.miao@outlook.com

2. Developement

Click: Used for building terminal command interaction.

Click website: https://github.com/pallets/click

Setuptools: Used for building Python module.

Setuptools website: https://github.com/pypa/setuptools

3. Install from PYPI for Python using PIP

FishRatio PYPI: Calculate the ratio and logarithmic value of species contained in several genus of a family to all species in this family.

https://pypi.org/project/fishratio

pip install fishratio

4. Fish Ratio Usage

Calculate the ratio and logarithmic value of species contained in several genus of a family to all species in this family

fishratio --help
Usage: fishratio [OPTIONS]

     Description:

     Calculate the ratio and logarithmic value of species contained in
     several genus of a family to all species in this family.

     Examples:

     1. Get options and parameters help:

     FishRatio --help

     2. Sample command with all default parameters:

     FishRatio --input input.xlsx     or

     FishRatio --input input.xlsx --ratio true --ln_ratio true --neg_ratio
     true --output output.xlsx

     3. Only calculate (species number of genus) / (species number of
     family):

     FishRatio --input input.xlsx --ratio true --ln_ratio false --neg_ratio
     false --output output.xlsx

Options:
  --input TEXT        Full name (path + name + extension) of input file.
                      default="input.xlsx"

  --ratio BOOLEAN     Formula: (species number of genus) / (species number of
                      family) ratio value. default=True

  --ln_ratio BOOLEAN  Formula: Log(e)(ratio value). default=True
  --neg_mul BOOLEAN   Formula: -(ratio x Log(e)(ratio value)). default=True
  --output TEXT       Full name (path + name + extension) of output file.
                      default="output.xlsx"

  --help              Show this message and exit.

5. Examples

Examples folder: path to miniconda: ./miniconda3/lib/site-packages/fishratio/examples/

# Sample command with all default parameters:

FishRatio --input input.xlsx
# or
FishRatio --input input.xlsx --ratio true --ln_ratio true --neg_ratio
true --output output.xlsx

input.xlsx

Family	Genus	Species
Myxinidae	Eptatretus	3
Chimaeridae	Chimaera	1
Chimaeridae	Hydrolagus	1
Scyliorhinidae	Apristurus	2
Scyliorhinidae	Atelomycterus	1
Scyliorhinidae	Cephaloscyllium	3
Scyliorhinidae	Galeus	1
Scyliorhinidae	Halaelurus	1
Scyliorhinidae	Parmaturus	1

output.xlsx

Family	Genus	Species	Ratios	LnRatio	NegMul
Chimaeridae	Chimaera	1	0.5	-0.693147181	0.34657359
Chimaeridae	Hydrolagus	1	0.5	-0.693147181	0.34657359
Myxinidae	Eptatretus	3	1	0	0
Scyliorhinidae	Apristurus	2	0.222222222	-1.504077397	0.334239422
Scyliorhinidae	Atelomycterus	1	0.111111111	-2.197224577	0.244136064
Scyliorhinidae	Cephaloscyllium	3	0.333333333	-1.098612289	0.366204096
Scyliorhinidae	Galeus	1	0.111111111	-2.197224577	0.244136064
Scyliorhinidae	Halaelurus	1	0.111111111	-2.197224577	0.244136064
Scyliorhinidae	Parmaturus	1	0.111111111	-2.197224577	0.244136064