Gnomonicus

Latest version: v2.5.7

Safety actively analyzes 638388 Python packages for vulnerabilities to keep your Python projects secure.

Scan your dependencies

Page 5 of 8

1.1.3

What's Changed
* Various improvements to tests. Now at 100% coverage by JeremyWesthead in https://github.com/oxfordmmm/gnomonicus/pull/7
* Fixed minority populations. Added extra tests for these by JeremyWesthead in https://github.com/oxfordmmm/gnomonicus/pull/8
* Add minor index parsing to the CLI script + various pandas index fixes by JeremyWesthead in https://github.com/oxfordmmm/gnomonicus/pull/9
* Explictly type cast pandas DataFrames to avoid FutureWarnings by JeremyWesthead in https://github.com/oxfordmmm/gnomonicus/pull/10


**Full Changelog**: https://github.com/oxfordmmm/gnomonicus/compare/v1.1.2...v1.1.3

1.1.2

Bump gumpy version
This pulls in a bug fix which was causing erroneous `InvaluidMutationException` to be raised when a deletion started in a promoter and passed the gene end

1.1.1

Updates to docker action to wait for PyPi to update before using it to build the new container

1.1.0

Removal of an unused argument to `populateEffects` causing a non-backwards compatible API change.

1.0.2

Due to changes to `gumpy`, this had to be updated to match.

When a synonymous mutation is found, there may be cases in which it is important to know specifically which nucleotides in the codon changed. For example, in the WHO catalogue, `fabG1L203L` has three different predictions depending on which nucleotides are changed:
If the change is `fabG1g609a`, it confers `R`
If the change is `fabG1c607t`, it confers `U`
If the change is anything else, it should confer `S` due to the default rule `gene*=` confers `S`

Therefore an update was made to include the nucleotide changes within each synonymous mutation. Within the WHO catalogue, this takes the form of all synonymous mutations being converted to multi-mutations with their nucleotide variants. This allows the above to be represented within single rows:
`fabG1L203L&fabG1g609a` confers `R`
`fabG1L203L&fabG1c607t` confers `U`
`fabG1L203L` confers `S`

`gumpy` was then updated to match this logic - pulling out such nucleotide variants for all synonymous mutations.

Within `gnomonicus` then, this results in nucleotide variants being mixed into the MUTATIONS in such cases, but these are excluded from the EFFECTS in every case other than when the associated multi-mutation lies within the catalogue. The result is that the nucleotide is never considered as a stand-alone mutation for the sake of EFFECTS, but is included as part of a multi-mutation iff the catalogue specifies this.

1.0.1

Now in a stable state. Full usage instructions can be found in `README.md`

Page 5 of 8

© 2024 Safety CLI Cybersecurity Inc. All Rights Reserved.