phenopacket-store-toolkit

Name	phenopacket-store-toolkit JSON
Version	0.1.4 JSON
	download
home_page	None
Summary	Collection of GA4GH Phenopackets
upload_time	2024-09-01 12:18:58
maintainer	None
docs_url	None
author	None
requires_python	>=3.10
license	BSD 3-Clause License Copyright (c) 2022, Monarch Initiative Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
keywords	global alliance for genomics and health ga4gh phenopacket schema human phenotype ontology ga4gh hpo
VCS
bugtrack_url
requirements	No requirements were recorded.
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            # Phenopacket Store Toolkit


Phenopacket Store Toolkit is a Python package and CLI 
for managing [Phenopacket Store](https://github.com/monarch-initiative/phenopacket-store), 
a collection of [GA4GH Phenopacket](https://phenopacket-schema.readthedocs.io/en/latest/) cohorts
that represent individuals with Mendelian diseases.

The toolkit aids the release and Q/C processes, 
and simplifies access to the Phenopacket Store data from the downstream applications.


## Availability

Phenopacket Store Toolkit can be installed from Python Package Index (PyPi):

```shell
python3 -m pip install phenopacket-store-toolkit
```

## Examples

### Access Phenopacket Store

The toolkit simplifies download and loading the cohort data. The `PhenopacketStoreRegistry` API
caches the release ZIP files locally (in `$HOME/.phenopacket-store` by default) 
and simplifies the loading:

```python
from ppktstore.registry import configure_phenopacket_registry

registry = configure_phenopacket_registry()

with registry.open_phenopacket_store(release="0.1.18") as ps:
   phenopackets = list(ps.iter_cohort_phenopackets("SUOX"))

assert len(phenopackets) == 35
```

The code checks if the release ZIP of Phenopacket Store version `0.1.18` is already 
available locally, and downloads the release ZIP file if necessary. 
This is followed by opening the store as `ps` 
and loading all phenopackets of the *SUOX* cohort.

We use Python context manager to ensure proper closing of the ZIP file handle.
`ps` *cannot* be used outside of the context manager block.

As an alternative to using a specific Phenopacket Store release, 
the *latest* release will be used if `release` argument is omitted.

### Make Phenopacket Store release

The release is handled by the Command Line Interface (CLI) of the toolkit.

The release functionality requires additional dependencies, which are installed automatically
by adding `release` profile:

```shell
python3 -m pip install phenopacket-store-toolkit[release]
```

Now, assuming that `notebooks` points to the notebook folder of the Phenopacket Store repository,
we can Q/C the phenopackets by running:

```shell
python3 -m ppktstore qc --notebook-dir notebooks
```

and we can create the release archive by running:

```shell
python3 -m ppktstore package --notebook-dir notebooks --release-tag 0.1.18 --output all_phenopackets
```

This will find all phenopackets in the `notebooks` folder, copy them into a top-level directory called `0.1.18`, 
and ZIP the directory into `all_phenopackets.zip`. 

## Learn more

Find more info in our detailed documentation:

- [Stable documentation](https://monarch-initiative.github.io/phenopacket-store-toolkit/stable) (last release on `main` branch)
- [Latest documentation](https://monarch-initiative.github.io/phenopacket-store-toolkit/latest) (bleeding edge, latest commit on `develop` branch)

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    "description": "# Phenopacket Store Toolkit\n\n\nPhenopacket Store Toolkit is a Python package and CLI \nfor managing [Phenopacket Store](https://github.com/monarch-initiative/phenopacket-store), \na collection of [GA4GH Phenopacket](https://phenopacket-schema.readthedocs.io/en/latest/) cohorts\nthat represent individuals with Mendelian diseases.\n\nThe toolkit aids the release and Q/C processes, \nand simplifies access to the Phenopacket Store data from the downstream applications.\n\n\n## Availability\n\nPhenopacket Store Toolkit can be installed from Python Package Index (PyPi):\n\n```shell\npython3 -m pip install phenopacket-store-toolkit\n```\n\n## Examples\n\n### Access Phenopacket Store\n\nThe toolkit simplifies download and loading the cohort data. The `PhenopacketStoreRegistry` API\ncaches the release ZIP files locally (in `$HOME/.phenopacket-store` by default) \nand simplifies the loading:\n\n```python\nfrom ppktstore.registry import configure_phenopacket_registry\n\nregistry = configure_phenopacket_registry()\n\nwith registry.open_phenopacket_store(release=\"0.1.18\") as ps:\n   phenopackets = list(ps.iter_cohort_phenopackets(\"SUOX\"))\n\nassert len(phenopackets) == 35\n```\n\nThe code checks if the release ZIP of Phenopacket Store version `0.1.18` is already \navailable locally, and downloads the release ZIP file if necessary. \nThis is followed by opening the store as `ps` \nand loading all phenopackets of the *SUOX* cohort.\n\nWe use Python context manager to ensure proper closing of the ZIP file handle.\n`ps` *cannot* be used outside of the context manager block.\n\nAs an alternative to using a specific Phenopacket Store release, \nthe *latest* release will be used if `release` argument is omitted.\n\n### Make Phenopacket Store release\n\nThe release is handled by the Command Line Interface (CLI) of the toolkit.\n\nThe release functionality requires additional dependencies, which are installed automatically\nby adding `release` profile:\n\n```shell\npython3 -m pip install phenopacket-store-toolkit[release]\n```\n\nNow, assuming that `notebooks` points to the notebook folder of the Phenopacket Store repository,\nwe can Q/C the phenopackets by running:\n\n```shell\npython3 -m ppktstore qc --notebook-dir notebooks\n```\n\nand we can create the release archive by running:\n\n```shell\npython3 -m ppktstore package --notebook-dir notebooks --release-tag 0.1.18 --output all_phenopackets\n```\n\nThis will find all phenopackets in the `notebooks` folder, copy them into a top-level directory called `0.1.18`, \nand ZIP the directory into `all_phenopackets.zip`. \n\n## Learn more\n\nFind more info in our detailed documentation:\n\n- [Stable documentation](https://monarch-initiative.github.io/phenopacket-store-toolkit/stable) (last release on `main` branch)\n- [Latest documentation](https://monarch-initiative.github.io/phenopacket-store-toolkit/latest) (bleeding edge, latest commit on `develop` branch)\n",
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