pandas-genomics-0.10.1.tar.gz

<div align="center"> <img src="https://github.com/HallLab/pandas-genomics/raw/master/docs/_static/logo.png" alt="pandas_genomics logo"/> </div> <br/> <div align="center"> <!-- Python version --> <a href="https://pypi.python.org/pypi/pandas-genomics"> <img src="https://img.shields.io/badge/python-3.7+-blue.svg?style=flat-square" alt="PyPI version"/> </a> <!-- PyPi --> <a href="https://pypi.org/project/pandas-genomics/"> <img src="https://img.shields.io/pypi/v/pandas-genomics.svg?style=flat-square" alt="pypi" /> </a><br> <!-- Build status --> <a href="https://github.com/HallLab/pandas-genomics/actions?query=workflow%3ACI"> <img src="https://img.shields.io/github/workflow/status/HallLab/pandas-genomics/CI?style=flat-square" alt="Build Status" /> </a> <!-- Docs --> <a href="https://pandas-genomics.readthedocs.io/en/latest/"> <img src="https://img.shields.io/readthedocs/pandas-genomics?style=flat-square" alt="Read the Docs" /> </a> <!-- Test coverage --> <a href="https://codecov.io/gh/HallLab/pandas-genomics/"> <img src="https://img.shields.io/codecov/c/gh/HallLab/pandas-genomics.svg?style=flat-square" alt="Coverage Status"/> </a><br> <!-- License --> <a href="https://opensource.org/licenses/BSD-3-Clause"> <img src="https://img.shields.io/pypi/l/pandas-genomics?style=flat-square" alt="license"/> </a> <!-- Black --> <a href="https://github.com/psf/black"> <img src="https://img.shields.io/badge/code%20style-Black-black?style=flat-square" alt="code style: black"/> </a> </div> <br/> Pandas ExtensionDtypes and ExtensionArray for working with genomics data Quickstart ---------- `Variant` objects holds information about a particular variant: ```python from pandas_genomics.scalars import Variant variant = Variant('12', 112161652, id='rs12462', ref='A', alt=['C', 'T']) print(variant) ``` rs12462[chr=12;pos=112161652;ref=A;alt=C,T] Each variant should have a unique ID, and a random ID is generated if one is not specified. `Genotype` objects are associated with a particular `Variant`: ```python gt = variant.make_genotype("A", "C") print(gt) ``` ``` A/C ``` The `GenotypeArray` stores genotypes with an associated variant and has useful methods and properties: ```python from pandas_genomics.scalars import Variant from pandas_genomics.arrays import GenotypeArray variant = Variant('12', 112161652, id='rs12462', ref='A', alt=['C']) gt_array = GenotypeArray([variant.make_genotype_from_str(s) for s in ["C/C", "A/C", "A/A"]]) print(gt_array) ``` ``` <GenotypeArray> [Genotype(variant=rs12462[chr=12;pos=112161652;ref=A;alt=C], allele1=1, allele2=1), Genotype(variant=rs12462[chr=12;pos=112161652;ref=A;alt=C], allele1=0, allele2=1), Genotype(variant=rs12462[chr=12;pos=112161652;ref=A;alt=C], allele1=0, allele2=0)] Length: 3, dtype: genotype[12; 112161652; rs12462; A; C] ``` ```python print(gt_array.astype(str)) ``` ``` ['C/C' 'A/C' 'A/A'] ``` ```python print(gt_array.encode_dominant()) ``` ``` <IntegerArray> [1.0, 1.0, 0.0] Length: 3, dtype: float ``` There are also `genomics` accessors for Series and DataFrame ```python import pandas as pd print(pd.Series(gt_array).genomics.encode_codominant()) ``` ``` 0 Hom 1 Het 2 Ref Name: rs12462_C, dtype: category Categories (3, object): ['Ref' < 'Het' < 'Hom'] ```