A Python API for managing genotype-phenotype map data
Project description
GPMap
A Python API for managing genotype-phenotype map data
GPMap defines a flexible object for managing genotype-phenotype (GP) map data. At it's core, it stores all data in Pandas DataFrames and thus, interacts seamlessly with the PyData egosystem.
To visualize genotype-phenotype objects created by GPMap, checkout GPGraph.
Basic example
Import the package's base object.
from gpmap import GenotypePhenotypeMap
Pass your data to the object.
# Data
wildtype = "AAA"
genotypes = ["AAA", "AAT", "ATA", "TAA", "ATT", "TAT", "TTA", "TTT"]
phenotypes = [0.1, 0.2, 0.2, 0.6, 0.4, 0.6, 1.0, 1.1]
stdeviations = [0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05]
# Initialize the object
gpm = GenotypePhenotypeMap(wildtype,
genotypes,
phenotypes,
stdeviations=stdeviations)
# Check out the data.
gpm.data
Or load a dataset from disk.
gpm = GenotypePhenotypeMap.read_json("data.json")
Installation
Users This simplest way to install this package is using pip:
pip install gpmap
Developers
The recommended way to install this package fro development is using pipenv
.
- Clone this repository:
git clone https://github.com/harmslab/gpmap
- Install the package using pipenv.
cd gpmap
pipenv install --dev -e .
- Run tests using pytest
pytest
Dependencies
The following modules are required. Also, the examples/tutorials are written in Jupyter notebooks and require IPython to be install.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for gpmap-0.5.0-py2.py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | e0651370fef967ff9d299736cd88ec623a06e80e052a96b4945143dcf7e1d898 |
|
MD5 | 35d8c2cb3316e26fa42c574c8e280bb9 |
|
BLAKE2b-256 | e20f9c89e660a56c840f6f7cc5e818e617a0f17b40e205692fd72d9c2cdcce93 |