v0.9.1-alpha4

Retrain internal model with:

$ python -m gecco -vv train --c1 0.4 --c2 0 --select 0.25 --window-size 20 \
         -f mibig-2.0.proG2.Pfam-v35.0.features.tsv \
         -c mibig-2.0.proG2.clusters.tsv \
         -g GECCO-data/data/embeddings/mibig-2.0.proG2.genes.tsv \
         -o models/v0.9.1-alpha4

v0.9.1-alpha3

Added

• gecco.model.GeneTable class to store gene coordinates independently of protein domains.

Changed

• Refactored implementation of load and dump methods for Table classes into a dedicated base class.
• gecco run and gecco annotate now output a gene table in addition to the feature and cluster tables.
• gecco train expects a gene table instead of a GFF file for the gene coordinates.

v0.9.1-alpha2

Fixed

• TypeClassifier.trained not being able to read unknown types from type tables.

v0.9.1-alpha1

Candidate release with support for a sliding window in the CRF prediction algorithm.

v0.8.10

Fixed

• --antismash-sideload flag of gecco run causing command to crash.

v0.8.9

Removed

• Prediction and support for the Other biosynthetic type of MIBiG clusters.

v0.8.8

Fixed

• ClusterRefiner filtering method for edge genes not working as intended.
• gecco run and gecco annotate commands crashing on missing input files instead of nicely rendering the error.

v0.8.7

Fixed

• interpro.json metadata file not being included in distribution files.
• Missing docstring for Protein.with_domains method.

Changed

• Bump minimum scikit-learn version to v1.0 for Python3.7+.

v0.8.6 - YANKED

Added

• CLI flag for enabling region masking for contigs processed by Prodigal.
• CLI flag for controlling region distance used for edge distance filtering.

Changed

• gecco.model.Gene and gecco.model.Protein are now immutable data classes.
• Bump minimum pyrodigal version to v0.6.4 to use region masking.
• Implement filtering for extracted clusters based on distance to the contig edge.
• Store InterPro metadata file uncompressed for version-control integration.

Fixed

• Mark BGC0000930 as Terpene in the type classifier data.
• Progress bar messages are now in consistent format.

0.8.5

Added

• Minimal compatibility support for running GECCO inside of Galaxy workflows.