All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Mash sketch files are now validated using MD5 checksum to ensure integrity
- Added
--table-pathoption tosearch-pangenomesto save TSV output to a file - Added
--no-tableflag to disable table output insearch-pangenomes list-collectionsnow automatically detects terminal vs redirected output: displays formatted table in interactive terminals, plain TSV when redirected to files or pipes
search-pangenomestable output now defaults to stdout instead of a file (previous default waspangenomes_information.tsv)
- Added
--tableoption to search-pangenomes for exporting results as a TSV table - Added a workflow to publish the package to PyPI in P
- Change the match-pangenome command option
--input_genomeby--input-genome - Updated dependencies:
pangbank-apiis now referenced from PyPI instead of a GitHub link in PR
- Search pangenomes by taxon, genome, or collection: Query PanGBank API to find relevant pangenomes matching specific criteria.
- Retrieve pangenome metrics: Access information on pangenomes, including taxonomy, number of genomes, gene counts, and other statistics.
- Download pangenome files: Fetch pangenome files directly from PanGBank for downstream analysis with PPanGGOLiN.
- Match an input genome to a pangenome: Identify the most similar pangenome to a given genome using mash sketches of the selected collection.