# PyMIP [![PyPI version][fury-image]][fury-url] [![Build Status][travis-image]][travis-url] Provides a Python API to manipulate the [MIP][mip] analysis pipeline: setup, starting, monitoring, and parsing output.
## Features
TODO
### Archive analysis After a case has been solved or abandoned it is necessary to wrap up the analysis and archive the results. Pymip will handle this task by bundling the most vital assets from the output and deleting the rest.
Assets that are kept:
CRAM file as a source of the raw (aligned) reads
BCF file as a source of all (unannotated) variants
QC metrics as a source for quality metrics
Pymip will not touch any of the files under “exomes/genomes” only “analysis”. Physically the files will be collected in a folder under “exomes/genomes” names “archive”. The script will also update the AnalysisRunStatus in the QC sample info file to Archived.
## Install for development
`bash $ pip install --editable . `
## Contributing Anyone can help make this project better - read [CONTRIBUTING](CONTRIBUTING.md) to get started!
## License MIT. See the [LICENSE](LICENSE) file for more details.
[fury-url]: http://badge.fury.io/py/pymip [fury-image]: https://badge.fury.io/py/pymip.png
[travis-url]: https://travis-ci.org/Clinical-Genomics/pymip [travis-image]: https://img.shields.io/travis/Clinical-Genomics/pymip.svg?style=flat
1 maintainer
Metadata
1 maintainer
Release files for pymip 0.2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| pymip-0.2.0.tar.gz | 7.0 MB | Without provenance | Details for pymip-0.2.0.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| pymip-0.2.0-py2.py3-none-any.whl | Python 3, Python 2 | none | any | Details for pymip-0.2.0-py2.py3-none-any.whl |
Total release size: 7.0 MB
Release files / pymip-0.2.0.tar.gz
| Download URL | pymip-0.2.0.tar.gz |
|---|---|
| Size | 7.0 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
6f9f03aa587b68c64527e68e0c33825418aac12eede999a59a1f176d53efa8c1
|
|
BLAKE2b-256 checksum How to use checksums |
de8203c5afbe227143a9bd1fa255af77209d87ba1b689fd04e64d2aa2423ad4f
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
Release files / pymip-0.2.0-py2.py3-none-any.whl
| Download URL | pymip-0.2.0-py2.py3-none-any.whl |
|---|---|
| Size | 18.3 kB |
| Tags | Python 2 Python 3 |
|
SHA-256 checksum How to use checksums |
886bfceb6a535228c7fcb6ef2eec8ab69199dc5db66c6ec9aa61829040c684fa
|
|
BLAKE2b-256 checksum How to use checksums |
b871135b29cc887b114d8a652ccb6b53b974c53a2cc2775dc2a5b594271a2391
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
Security for pymip 0.2.0
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
