ciscorucinski / pango_aliasor

Utility to compress and uncompress PANGO lineage aliases

Python convenience library to translate between aliased and unaliased Pango lineages

Useful for:

• constructing a tree of Pango lineages
• semantic sorting of Pango lineages
• ...

Usage

from pango_aliasor.aliasor import Aliasor

# Initalize aliasor (only needs to be done once)
# If no alias_key.json is passed, downloads the latest version from github
aliasor = Aliasor()

# To use custom alias_key.json, pass the relative path to the file
# aliasor = Aliasor('alias_key.json')

# Go from aliased lineage to unaliased lineage
aliasor.uncompress("BA.5") # 'B.1.1.529.5'
aliasor.uncompress("BE.5") # 'B.1.1.529.5.3.1.5'
aliasor.uncompress("XA") # 'XA'

# Go from unaliased lineage to aliased lineage
aliasor.compress("B.1.1.529.3.1") # 'BA.3.1'

aliasor.partial_compress("B.1.1.529.3.1",up_to=1) # 'BA.3.1'
aliasor.partial_compress("B.1.1.529.3.1.1.2",up_to=1) # 'BA.3.1.1.2'

aliasor.partial_compress("B.1.1.529.3.1",accepted_aliases=["AY"]) # 'B.1.1.529.3.1'
aliasor.partial_compress("B.1.617.2",accepted_aliases=["AY"]) # 'AY.2'

aliasor.partial_compress('B.1.1.529.2.75.1.2',up_to=4, accepted_aliases={"BA"}) == 'BL.2'

See tests for more examples.

Installation

pip install pango_aliasor

Testing

Run pytest from the project root to run all tests.

Release

1. Bump version in setup.cfg
2. Release using gh release create
3. Build using python3 -m build
4. Publish to Pypi using twine upload dist/pango_aliasor*