airpg: Automatically accessing the inverted repeats of archived plastid genomes

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: 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: 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: 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

Tutorial 4: 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

CHANGELOG

See CHANGELOG.md for a list of recent changes to the software.