v1.2.0

Snekmer 1.2.0 Release Notes

Description

The Snekmer v1.2.0 release primarily includes the new Snekmer Learn and Snekmer Apply pipelines, which allow users to evaluate the confidence of kmers in annotation and use the learned information to annotate unknown sequences. This release also include code refactoring to fix memory leakage issues in the clustering workflow, remove obsolete/legacy code and specifications, simplify versioning, resolve bugs.

What's Changed

• Merged in new fixes from main by @biodataganache in #68
• updates by @biodataganache in #76
• Kmer association by @jjacobson95 in #109
• docs: change base class for SnekmerModel by @christinehc in #111
• Kmer association by @jjacobson95 in #115

Full Changelog: v1.0.4...v1.2.0

Contributors

• Jeremy Jacobson (@jjacobson95) - primary code development
• Christine Chang (@christinehc) - code development
• Jason McDermott (@biodataganache) - code development supervision
• Bill Nelson (@wichne) - subject matter expert

v1.0.4

Snekmer v1.0.4 Release Notes

The Snekmer v1.0.4 release includes minor code refactoring to directly call the flexible SnekmerModel object rather than fixing the model type to logistic regression. All Snekmer-generated objects now also store the Snekmer version number as an attribute, important for reproducibility in analytical workflows involving Snekmer.

Changelog

Description

• snekmer.model.SnekmerModel is now used to build models, with the default model type remaining as "logistic".
• Snekmer version numbers are stored as attributes in the snekmer.score.KmerScoreScaler, snekmer.vectorize.KmerBasis, and snekmer.vectorize.KmerVec objects (as self.snekmer_version).

What's Changed

• [docs] Add Apple silicon / additional instructions by @christinehc in #103
• [chore] merge main changes into branch by @christinehc in #104
• Update README.md by @lnanderson in #106
• chore: combine branches by @christinehc in #107
• Model version by @christinehc in #105

Contributors

• Christine Chang (@christinehc) - code development
• Bill Nelson (@wichne) - feature request
• Jason McDermott (@biodataganache)
• Jeremy Jacobson (@jjacobson95)

New Contributors

• @lnanderson made their first contribution in #106

Full Changelog: v1.0.3...v1.0.4

v1.0.3

Snekmer v1.0.3 Release Notes

The Snekmer v1.0.3 release includes code refactoring and some changes to improve usability, including improving documentation and logged error messages, updating CI to directly install and execute Snekmer for better error catching, and restricting some CLI arguments to minimize errors.

Changelog

Major Changes

• Certain snakemake args (--configfile, --cores) no longer produce errors under default conditions.
• Documentation updates now include instructions for the Snekmer Docker container.
• Snekmer prevents automated model-building for files containing an insufficient number of sequences.
• GitHub actions (CLI) workflow now captures the full installation and code execution process instead of indirect testing via calling individual Snakefiles.
• Where appropriate, run directive has been replaced with script directive to reduce Snakefile size and make formatting/linting/debugging easier.

Minor Changes

• Documentation has been updated, particularly for troubleshooting.
• Nested output directory option is now working again.
• Minor docstring/type hinting updates

Contributors

• Christine Chang (@christinehc)
• Jason McDermott (@biodataganache)
• Jeremy Jacobson (@jjacobson95)

v1.0.0-beta

Changelog

Major Changes

• Overhaul to kmerize.smk: Now proceeds through a bag-of-words and generator-based approach to reduce memory requirements. Affects snekmer cluster, snekmer model, and snekmer search.
• Overhaul to snekmer cluster: Clustering methods and distance matrix computation methods are updated. Now includes option to invoke BSF.
• Tutorial has been overhauled to reflect code changes

Minor Changes

• Documentation now exists via snekmer.readthedocs.io
• Updates/fixes to address the large memory requirements of snekmer cluster
• Installation instructions updated to account for various software ecosystems

Contributors

• Christine Chang (@christinehc)
• Jason McDermott (@biodataganache)
• Abby Jerger (@abbyjerger)

v0.1.2-beta

Changelog

• Updated clustering module for compatibility with changes to snekmer.cluster.KmerClustering object, snekmer.transform, and kmerize.smk
• Cluster now works locally with small test example

v0.1.1-beta

Snekmer v0.1.1-beta

Changelog

• Enable nested directory output structure for snekmer search mode
  • e.g. output/model/family.pkl -> output/model/{alphabet}/{k}/model/family.pkl
• Update code formatting/style for all .py and .smk (snakemake) files

v0.1.0-beta

About

Beta release of Snekmer as described in "Snekmer: A scalable pipeline for protein sequence fingerprinting based on amino acid recoding" (2022)

Contributors

• Christine Chang (@christinehc)
• Jason McDermott (@biodataganache)
• Bill Nelson (@wichne)