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 for 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 installed.
Release files for gpmap 0.7.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| gpmap-0.7.0.tar.gz | 136.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| gpmap-0.7.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 160.2 kB
Release files / gpmap-0.7.0.tar.gz
| Download URL | gpmap-0.7.0.tar.gz |
|---|---|
| Size | 136.2 kB |
| Tags | Source |
|
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Release files / gpmap-0.7.0-py3-none-any.whl
| Download URL | gpmap-0.7.0-py3-none-any.whl |
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| Tags | Python 3 |
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