Calculate the ratio and logarithmic value of species contained in several genus of a family to all species in this family.
Project description
1. Author Information
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 |
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