https://github.com/harmslab/gpmap

A Python API for managing genotype-phenotype map data
https://github.com/harmslab/gpmap

evolution genetics genotype-phenotype-maps networkx

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A Python API for managing genotype-phenotype map data

• Host: GitHub
• URL: https://github.com/harmslab/gpmap
• Owner: harmslab
• Created: 2015-07-24T20:21:38.000Z (over 10 years ago)
• Default Branch: main
• Last Pushed: 2023-08-18T18:26:41.000Z (over 2 years ago)
• Last Synced: 2025-12-26T23:58:26.479Z (3 months ago)
• Topics: evolution, genetics, genotype-phenotype-maps, networkx
• Language: Python
• Homepage:
• Size: 1.42 MB
• Stars: 12
• Watchers: 9
• Forks: 8
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

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README

          

# GPMap

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[![nbviewer](https://raw.githubusercontent.com/jupyter/design/master/logos/Badges/nbviewer_badge.svg)](https://nbviewer.jupyter.org/github/harmslab/gpmap/blob/master/examples/Introduction%20to%20Genotype-Phenotype%20Map%20Module.ipynb#)

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*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 ecosystem.

To visualize genotype-phenotype objects created by GPMap, checkout [GPGraph](https://github.com/Zsailer/gpgraph).

 

## Basic example

Import the package's base object.

```python

from gpmap import GenotypePhenotypeMap

```

Pass your data to the object.

```python

# 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.

```python

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`.

1. Clone this repository:

```

git clone https://github.com/harmslab/gpmap

```

2. Install the package using pipenv.

```

cd gpmap

pipenv install --dev -e .

```

3. 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.

* [Numpy](http://www.numpy.org/)

* [Pandas](https://pandas.pydata.org/)