Gnomonicus

Latest version: v2.6.3

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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`

1.0.0beta.2

Actions fixes

1.0.0beta

Beta pre-release for testing GH actions for auto-publishing via Docker and PyPI

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