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.

Numpy
Pandas

Release files for gpmap 0.4.5

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for gpmap 0.4.5
File	Size	Uploaded
gpmap-0.4.5.tar.gz	18.4 kB	Oct 1, 2018	Details

Built distribution (wheel)

Table of built distributions (wheels) for gpmap 0.4.5
File	Interpreter	ABI	Platform	Reset
gpmap-0.4.5-py2.py3-none-any.whl 32.5 kB Oct 1, 2018	Python 2, Python 3	none	any	Details

Total release size: 51.0 kB

Release files / gpmap-0.4.5.tar.gz

Download URL	gpmap-0.4.5.tar.gz
Size	18.4 kB
Tags	Source
SHA-256 checksum How to use checksums	`6e8951fa8f78eaf508a1a6bf700ecf8584ff99e17d3fe9d6d7b4184bec6446da`
BLAKE2b-256 checksum How to use checksums	`b6ee22ac0a310878280492aab888f1b0009c36ac67ea3d55b9b359adae1474de`
Upload date	Oct 1, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/40.2.0 requests-toolbelt/0.8.0 tqdm/4.23.4 CPython/3.6.5`

Release files / gpmap-0.4.5-py2.py3-none-any.whl

Download URL	gpmap-0.4.5-py2.py3-none-any.whl
Size	32.5 kB
Tags	Python 2 Python 3
SHA-256 checksum How to use checksums	`eb3c9b3757c26b3ebc7466509f690e939429c8f7bc2e8090130fffbadb647101`
BLAKE2b-256 checksum How to use checksums	`256e9172cb931bdc81233ed323dc3f6e9c92d873cd0054a43f0d8a8a06e356d6`
Upload date	Oct 1, 2018
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/1.11.0 pkginfo/1.4.2 requests/2.19.1 setuptools/40.2.0 requests-toolbelt/0.8.0 tqdm/4.23.4 CPython/3.6.5`