Generate and work with GA4GH phenopackets

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ielis from gravatar.com ielis Avatar for pnrobinson from gravatar.com pnrobinson

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: MIT License (MIT License Copyright (c) 2023, The Monarch Initiative Permission is hereby granted, free of charg...)
  • Author: Peter Robinson
  • Tags Global Alliance for Genomics and Health, GA4GH Phenopacket Schema, Human Phenotype Ontology, GA4GH, HPO
  • Requires: Python >=3.5
Classifiers

Project description

pyphetools

Python Phenopacket Tools

This package currently is designed to test how to use the Python version of the phenopackets package together with pandas to create phenopackets from typical supplemental tables.

Development goals include making builder code similar to the Java package to create valid phenopackets and to perform JSON Schema-based validation.

Setup

For initial development, we will use notebooks mainly. Do the following to get set up. Note that now we are using phenopackets version 2.0.2. openpyxl is needed to read Excel files.

python3 -m venv venv
source venv/bin/activate
pip install -r requirements.txt
pip install jupyter
python -m ipykernel install --name "venv" --display-name "venv"
cd notebooks
jupyter-notebook

We have installed the package in the Python Package Index (pypi) at pyphentools.

Updating package in PyPI

Make sure the build and twine packages are installed.

python3 -m pip install --upgrade build
python3 -m pip install --upgrade twine

Update the version number in the pyproject.toml file Build and install

python3 -m build
python3 -m twine upload dist/*

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ielis from gravatar.com ielis Avatar for pnrobinson from gravatar.com pnrobinson

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: MIT License (MIT License Copyright (c) 2023, The Monarch Initiative Permission is hereby granted, free of charg...)
  • Author: Peter Robinson
  • Tags Global Alliance for Genomics and Health, GA4GH Phenopacket Schema, Human Phenotype Ontology, GA4GH, HPO
  • Requires: Python >=3.5
Classifiers

Release history Release notifications | RSS feed

0.9.113

0.9.112

0.9.111

0.9.110

0.9.109

0.9.108

0.9.107

0.9.106

0.9.105

0.9.104

0.9.103

0.9.102

0.9.101

0.9.100

0.9.99

0.9.98

0.9.97

0.9.96

0.9.95

0.9.94

0.9.93

0.9.92

0.9.91

0.9.90

0.9.89

0.9.88

0.9.86

0.9.85

0.9.84

0.9.83

0.9.82

0.9.81

0.9.80

0.9.79

0.9.78

0.9.77

0.9.76

0.9.75

0.9.74

0.9.71

0.9.70

0.9.69

0.9.67

0.9.66

0.9.65

0.9.64

0.9.63

0.9.62

0.9.61

0.9.60

0.9.58

0.9.57

0.9.56

0.9.54

0.9.53

0.9.52

0.9.51

0.9.49

0.9.48

0.9.47

0.9.46

0.9.45

0.9.44

0.9.43

0.9.42

0.9.41

0.9.40

0.9.39

0.9.38

0.9.37

0.9.36

0.9.35

0.9.34

0.9.33

0.9.32

0.9.31

0.9.29

0.9.28

0.9.27

0.9.26

0.9.25

0.9.24

0.9.22

0.9.21

0.9.20

0.9.17

0.9.16

0.9.15

0.9.13

0.9.12

0.9.11

0.9.9

0.9.8

0.9.7

0.9.6

0.9.4

0.9.3

0.9.2

0.9.1

0.8.31

0.8.30

0.8.29

0.8.28

0.8.27

0.8.26

0.8.25

0.8.24

0.8.23

0.8.22

0.8.21

0.8.20

0.8.19

0.8.18

0.8.17

0.8.16

0.8.15

0.8.14

0.8.13

0.8.12

0.8.11

0.8.10

0.8.8

0.8.7

0.8.3

0.8.2

0.8.1

0.7.5

0.7.4

0.7.3

0.7.2

0.7.1

0.6.6

0.6.5

0.6.4

0.6.3

0.6.2

0.6.1

0.5.11

0.5.10

0.5.8

0.5.7

0.5.5

0.5.4

0.5.3

0.5.2

0.5.1

0.4.16

0.4.15

0.4.14

0.4.13

0.4.12

0.4.11

0.4.9

0.4.8

0.4.7

0.4.5

0.4.1

0.4.0

0.3.6

0.3.5

0.3.4

0.3.3

0.3.2

0.3.1

0.3.0

0.2.27

0.2.26

0.2.25

0.2.24

0.2.23

0.2.22

0.2.21

0.2.20

0.2.19

0.2.18

0.2.17

0.2.16

0.2.15

0.2.14

0.2.13

0.2.12

0.2.11

0.2.10

0.2.9

0.2.7

This version

0.2.6

0.2.5

0.2.4

0.2.3

0.2.2

0.2.1

0.2.0

0.1.2

0.1.1

0.1.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyphetools-0.2.6.tar.gz (28.1 kB view details)

Uploaded Source

Built Distribution

pyphetools-0.2.6-py3-none-any.whl (35.9 kB view details)

Uploaded Python 3

File details

Details for the file pyphetools-0.2.6.tar.gz.

File metadata

  • Download URL: pyphetools-0.2.6.tar.gz
  • Upload date:
  • Size: 28.1 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.10.6

File hashes

Hashes for pyphetools-0.2.6.tar.gz
Algorithm Hash digest
SHA256 a3c8899dd97c38586459c788df64233d4a19d878b2c6282b3ea79cb17bb0d969
MD5 6e3ab424c206a30d96df7f67b365c4cc
BLAKE2b-256 1cb63e36e19ec0c09eae9b7de43ff1a74ddb0ac080c848aa2cb9cbe98279726e

See more details on using hashes here.

File details

Details for the file pyphetools-0.2.6-py3-none-any.whl.

File metadata

  • Download URL: pyphetools-0.2.6-py3-none-any.whl
  • Upload date:
  • Size: 35.9 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.10.6

File hashes

Hashes for pyphetools-0.2.6-py3-none-any.whl
Algorithm Hash digest
SHA256 58bef937b6c9dbe12e17aa20066041e3a968a9da2ea1097621f8a5bdf30791d8
MD5 34d5c13acd35b9e6b75d8c4cda91c215
BLAKE2b-256 13a4d4d9dd2a9a2ed686e6ee2380e5959e92cc75457e48877d4cdf014224b751

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page