v0.9.10

Fixed

• Progress reading display when reading from compressed files.
• Change labeling routine to use broad overlaps when annotating genes with cluster tables (#15).

Changed

• Bump supported polars dependency to v0.20.
• Bump supported statsmodels dependency to v0.14.
• Report identifier of sequences with uni-valued labels when training.

v0.9.9

Added

• Support for gzip, bzip2, lz4 and xz-compressed input files.

Fixed

• Outdated use of pandas API in gecco cv command.

Changed

• Bump pyhmmer dependency to v0.10.0.
• Bump pyrodigal dependency to v3.0.0.
• Make gecco cv output a gene table with a ground truth column.

v0.9.8

Fixed

• ClusterTable.from_clusters extracting cluster IDs in the wrong column.
• Deprecation warnings in polars.read_csv and polars.write_csv with recent polars versions.
• Deprecation warnings in importlib_resources with recent Python versions.

v0.9.7

Added

• Command line option to annotate proteins using bitscore cutoffs from HMMs.
• Command line option to disentangle overlapping domains after HMM annotation.

Changed

• Bump pyhmmer dependency to v0.8.0.
• Bump pyrodigal dependency to v2.1.0.
• Rewrite gecco.model to use polars for managing tabular data.
• Replace pandas dependencies with polars
• Update gecco run to skip type classification for tasks without an assigned cluster type.

Fixed

• Cluster.to_seq_record crashing when called on a cluster with types attribute unset.
• Progress bar resetting when performing domain annotation with multiple HMMs.

Removed

• Support for Python 3.7.

v0.9.6

Added

• Gene Ontology annotations to gecco.interpro local metadata.
• Reference to Gene Ontology terms and derived functions to gecco.model.Domain objects.
• Gene color based on predicted function in gecco.model.Gene.to_seq_feature.

Fixed

• Missing gzip import in the CLI preventing usage of gzip-compressed inputs.
• Invalid coordinates of domains found in reverse-strand genes.
• Detection of entry points with importlib.metadata on older Python versions.

Changed

• bgc_id columns of cluster tables are renamed cluster_id.
• gecco.model.ProductType is renamed to gecco.model.ClusterType.
• Bumped pyrodigal dependency to v2.0.
• Bumped pyhmmer dependency to v0.7.

v0.9.5

Added

• gecco predict command to predict BGCs from an annotated genome.
• Protein.with_seq function to assign a new sequence to a protein object.

Fixed

• Issue with antiSMASH sideload JSON file generation in gecco run and gecco predict.
• Make gecco.orf handle STOP codons consistently (#9).

v0.9.4

Added

• classes_ property to TypeClassifier to access the classes_ attribute of the TypeBinarizer.
• Alternative ORF finder CDSFinder which simply extracts CDS features from input sequences (#8).
• Support for annotating domains with "exclusive" HMMs to annotate genes with at most one HMM from the library.

Changed

• ProductType is not restricted to MIBiG types anymore and can support any string as a base type identifier.
• PyrodigalFinder now uses multiprocessing.pool.ThreadPool instead of custom thread code thanks to OrfFinder.find_genes reentrancy introduced in Pyrodigal v1.0.
• PyrodigalFinder can now be used in single / non-meta mode from the API.
• BUmped minimum rich version to 12.3 to use None total in progress bars when the size of an HMM library is unknown.

Fixed

• Broken MyPy type annotations in the gecco.model and gecco.cli modules.

v0.9.3

Changed

• --format flag of gecco annotate and gecco run CLI commands is now made lowercase before giving value to Bio.SeqIO.

Fixed

• Genes with duplicate IDs being silently ignored in HMMER.run.

v0.9.2

Added

• Padding of short sequences with empty genes when predicting probabilities in ClusterCRF.

v0.9.1

Changed

• Make the genes.tsv and features.tsv table contain all genes even when they come from a contig too short to be processed by the CRF sliding window.
• Replaced the --force-clusters-tsv flag with a --force-tsv flag to force writing TSV tables even when no genes or clusters were found in gecco run or gecco annotate.