Metadata-Version: 2.1
Name: airpg
Version: 1.1.4
Summary: A package to automatically access the inverted repeats of archived plastid genomes
Home-page: https://github.com/michaelgruenstaeudl/airpg
Author: Michael Gruenstaeudl, Tilman Mehl
Author-email: m.gruenstaeudl@fu-berlin.de, tilmanmehl@zedat.fu-berlin.de
License: GPLv3
Keywords: plastid genomes,inverted repeats,NCBI Nucleotide
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: POSIX
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: biopython
Requires-Dist: ete3
Requires-Dist: entrezpy
Requires-Dist: pandas
Requires-Dist: fuzzywuzzy
Requires-Dist: coloredlogs
Requires-Dist: python-Levenshtein

*airpg*: Automatically accessing the inverted repeats of archived plastid genomes
=================================================================================

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A Python package for automatically accessing the inverted repeats of thousands of plastid genomes stored on NCBI Nucleotide

## INSTALLATION
To get the most recent stable version of *airpg*, run:

    pip install airpg

Or, alternatively, if you want to get the latest development version of *airpg*, run:

    pip install git+https://github.com/michaelgruenstaeudl/airpg.git


## EXAMPLE USAGE


### [Tutorial 1](https://github.com/michaelgruenstaeudl/airpg/tree/main/airpg/tutorials/tutorial1.md): Very short survey (runtime ca. 5 min.; for the impatient)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide within the past 10 days.


### [Tutorial 2](https://github.com/michaelgruenstaeudl/airpg/tree/main/airpg/tutorials/tutorial2.md): Short survey (runtime ca. 15 min.; for testing)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide within the current month.


### [Tutorial 3](https://github.com/michaelgruenstaeudl/airpg/tree/main/airpg/tutorials/tutorial3.md): Medium survey (runtime ca. 5 hours)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide in 2019 only. Note: The results of this survey are available on Zenodo via DOI [10.5281/zenodo.4335906](https://zenodo.org/record/4335906)


### [Tutorial 4](https://github.com/michaelgruenstaeudl/airpg/tree/main/airpg/tutorials/tutorial4.md): Full survey (runtime ca. 19 hours; with explanations)
Survey of all plastid genomes of flowering plants submitted to NCBI Nucleotide from January 2000 until, and including, December 2020. Note: The results of this survey are available on Zenodo via DOI [10.5281/zenodo.4335906](https://zenodo.org/record/4335906)



<!--
## PACKAGING INSTRUCTIONS
```
#pip install .  ## For local testing

python3 -m build
python3 -m twine upload --repository testpypi dist/*
python3 -m pip install --index-url https://test.pypi.org/simple/ --no-deps airpg

python3 -m twine upload dist/*
python3 -m pip install airpg
```
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## CHANGELOG
See [`CHANGELOG.md`](CHANGELOG.md) for a list of recent changes to the software.


