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

This version

0.2.11

0.2.10

0.2.9

0.2.7

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-0.2.11.tar.gz (34.2 kB view details)

Uploaded Source

Built Distribution

pyphetools-0.2.11-py3-none-any.whl (45.8 kB view details)

Uploaded Python 3

File details

Details for the file pyphetools-0.2.11.tar.gz.

File metadata

  • Download URL: pyphetools-0.2.11.tar.gz
  • Upload date:
  • Size: 34.2 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.10.6

File hashes

Hashes for pyphetools-0.2.11.tar.gz
Algorithm Hash digest
SHA256 4bc7ab4d57f87a85073c6fae754e56d9fb48b493f29f7f2a2ebc4517b73452ce
MD5 2d848db6a4db819e73229d6aaeb78c81
BLAKE2b-256 93eb996b9f014a942986b0df102725b84a9eadaa6c90623bfac032d288a017a5

See more details on using hashes here.

File details

Details for the file pyphetools-0.2.11-py3-none-any.whl.

File metadata

  • Download URL: pyphetools-0.2.11-py3-none-any.whl
  • Upload date:
  • Size: 45.8 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.10.6

File hashes

Hashes for pyphetools-0.2.11-py3-none-any.whl
Algorithm Hash digest
SHA256 a482077d327a78bacdaa43cd2b2ad5704dc3d45bc6e6575b925c654a4c135648
MD5 24db33ad032b43f7951425fe26333680
BLAKE2b-256 f7ea319c2f586031943b175f30d63869d80981a9b2414316969bb4e3596fa52a

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