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Recent Releases of gecco-tool

gecco-tool - v0.10.0-alpha.3

Added

  • Support for changing the CLI argument defaults from a call to the gecco.cli.main function.

- Python
Published by github-actions[bot] 6 months ago

gecco-tool - v0.10.0-alpha.2

Fixed

  • gecco.cli and gecco.crf submodules not being included in wheel distribution.

- Python
Published by github-actions[bot] 6 months ago

gecco-tool - v0.10.0-alpha.1

Changed

  • Add an error in gecco convert when given input is not a folder.
  • Update numpy, polars, pyhmmer and psutil to latest versions.
  • Replace docopt with argparse parser for CLI argument parsing.
  • Make embedded_hmms generic over the module name.
  • Make ClusterCRF.trained accept any traversable.
  • Allow changing the default ClusterCRF and TypeClassifier classes used in gecco.cli.

Fixed

  • gecco convert issue when given a relative path.
  • Unused tqdm import in gecco.crf module.
  • Unused build dependencies from setup.cfg and pyproject.toml.
  • rich optional import logic in setup.py.

- Python
Published by github-actions[bot] 6 months ago

gecco-tool - 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.

- Python
Published by github-actions[bot] almost 2 years ago

gecco-tool - 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  • Outdated use of pandas API in gecco cv command.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.

- Python
Published by github-actions[bot] over 2 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] over 2 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] over 2 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] about 3 years ago

gecco-tool - 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).

- Python
Published by github-actions[bot] over 3 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] over 3 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] almost 4 years ago

gecco-tool - v0.9.2

Added

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

- Python
Published by github-actions[bot] almost 4 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] almost 4 years ago

gecco-tool - 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

- Python
Published by github-actions[bot] almost 4 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] almost 4 years ago

gecco-tool - v0.9.1-alpha2

Fixed

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

- Python
Published by github-actions[bot] almost 4 years ago

gecco-tool - v0.9.1-alpha1

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

- Python
Published by github-actions[bot] almost 4 years ago

gecco-tool - v0.8.10

Fixed

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

- Python
Published by github-actions[bot] about 4 years ago

gecco-tool - v0.8.9

Removed

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

- Python
Published by github-actions[bot] about 4 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] about 4 years ago

gecco-tool - 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+.

- Python
Published by github-actions[bot] about 4 years ago

gecco-tool - 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.

- Python
Published by github-actions[bot] about 4 years ago

gecco-tool - 0.8.5

Added

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

- Python
Published by althonos over 4 years ago

gecco-tool - 0.8.4

Fixed

  • gecco convert gbk --format bigslice failing to run because of outdated code (#5).
  • gecco convert gbk --format bigslice not creating files with names conforming to BiG-SLiCE expected input. ### Changed
  • Bump minimum pyrodigal version to v0.6.2 to use platform-accelerated code if supported.

- Python
Published by althonos over 4 years ago

gecco-tool - 0.8.3-post1

Fixed

  • Wrong default value for --threshold being shown in gecco run help message.

- Python
Published by althonos over 4 years ago

gecco-tool - 0.8.3

Changed

  • Default probability threshold for segmentation to 0.3 (from 0.4).

- Python
Published by althonos over 4 years ago

gecco-tool - 0.8.2

Fixed

  • gecco run crashing on Python 3.6 because of missing contextlib.nullcontext class. ### Changed
  • gecco run and gecco annotate will not try to count the number of profiles when given an external HMM file with the --hmm flag.
  • PyHMMER.run now reports the p-value of each domain in addition to the e-value as a /note qualifier.

- Python
Published by althonos over 4 years ago

gecco-tool - 0.8.1

Changed

  • gecco run now filters out unneeded features before annotating, making it easier to analyze the results of a run with a custom --model. ### Fixed
  • gecco reporting about using Pfam v33.1 while actually using v34.0 because of an outdated field in gecco/hmmer/Pfam.ini. ### Added
  • Missing documentation for the strand attribute of gecco.model.Gene.

- Python
Published by althonos over 4 years ago

gecco-tool - 0.8.0

Changed

  • Retrain internal model using new sequence embeddings and remove broken/duplicate BGCs from MIBiG 2.0.
  • Bump minimum pyhmmer version to v0.4.0 to improve exception handling.
  • Bump minimum pyrodigal version to v0.5.0 to fix sequence decoding on some platforms.
  • Use p-values instead of e-values to filter domains obtained with HMMER.
  • gecco cv and gecco train now seed the RNG with a user-defined seed before shuffling rows of training data. ### Fixed
  • Extraction of BGC compositions for the type predictor while training.
  • ClusterCRF.trained failing to open an external model. ### Added
  • Domain.pvalue attribute to access the p-value of a domain annotation.
  • Mandatory pvalue column to FeatureTable objects.
  • Support for loading several feature tables in gecco train and gecco cv.
  • Warnings to ClusterCRF.fit when selecting uninformative features.
  • --correction flag to gecco train and gecco cv, allowing to give a multiple testing correction method when computing p-values with the Fisher Exact Tests. ### Removed
  • Outdated gecco embed command.
  • Unused --truncate flag from the gecco train CLI.
  • Tigrfam domains, which is not improving performance on the new training data.

- Python
Published by althonos over 4 years ago

gecco-tool - 0.7.0

Added

  • Support for writing an AntiSMASH sideload JSON file after a gecco run workflow.
  • Code for converting GenBank files in BiG-SLiCE compatible format with the gecco convert subcommand.
  • Documentation about using GECCO in combination with AntiSMASH or BiG-SLiCE. ### Changed
  • Minimum Biopython version to v1.73 for compatibility with older bioinformatics tooling.
  • Internal domain composition shipped in the gecco.types with newer composition array obtained directly from MIBiG files. ### Removed
  • Outdated notice about -vvv verbosity level in the help message of the main gecco command.

- Python
Published by althonos over 4 years ago

gecco-tool - 0.6.3

Fixed

  • HMMER annotation not properly handling inputs with multiple contigs.
  • Some progress bar totals displaying as floats in the CLI. ### Changed
  • PyHMMER now sets the Z and domZ values from the number of proteins given to the search pipeline.
  • gecco.cli delegates imports to make CLI more responsive.
  • pkg_resources has been replaced with importlib.resources and importlib.metadata where applicable.
  • multiprocessing.cpu_count has been replaced with os.cpu_count where applicable.

- Python
Published by althonos almost 5 years ago

gecco-tool - 0.6.2

Fixed

  • gecco cv loto crashing because of outdated code. ### Changed
  • Logging-style prompt will only display if GECCO is running with -vv flag. ### Added
  • GECCO bioRxiv paper reference to Cluster.to_seq_record output record.

- Python
Published by althonos almost 5 years ago

gecco-tool - 0.6.1

Fixed

  • Progress bar not being disabled by -q flag in CLI.
  • Fallback to using HMM name if accession is not available in PyHMMER.
  • Group genes by source contig and process them separately in PyHMMER to avoid bogus E-values. ### Added
  • psutil dependency to get the number of physical CPU cores on the host machine.
  • Support for using an arbitrary mapping of positives to negatives in gecco embed. ### Removed
  • Unused and outdated HMMER and DomainRow classes from gecco.hmmer.

- Python
Published by althonos almost 5 years ago

gecco-tool - 0.6.0

Changed

  • Updated internal model with a cleaned-up version of the MIBiG-2.0 Pfam-33.1/Tigrfam-15.0 embedding.
  • Updated internal InterPro catalog. ### Fixed
  • Features not being grouped together in gecco cv and gecco train when provided with a feature table where rows were not sorted by protein IDs.

- Python
Published by althonos almost 5 years ago

gecco-tool - 0.5.5

Fixed

  • gecco cv bug causing only the last fold to be written.

- Python
Published by althonos almost 5 years ago

gecco-tool - 0.5.4

Changed

  • Replaced verboselogs, coloredlogs and better-exceptions with rich. ### Removed
  • tqdm training dependency. ### Added
  • gecco annotate command to produce a feature table from a genomic file.
  • gecco embed to embed BGCs into non-BGC regions using feature tables.

- Python
Published by althonos almost 5 years ago

gecco-tool - 0.5.3

Fixed

  • Coordinates of genes in output GenBank files.
  • Potential issue with the number of CPUs in PyHMMER.run. ### Changed
  • Bump required pyrodigal version to v0.4.2 to fix buffer overflow.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.5.2

Added

  • Support for downloading HMM files directly from GitHub releases assets.
  • Validation of filtered HMMs with MD5 checksum. ### Fixed
  • Invalid coordinates of protein domains in GenBank output files.
  • gecco.interpro module not being added to wheel distribution. ### Changed
  • Bump required pyhmmer version to v0.2.1.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.5.1

Fixed

  • --hmm flag being ignored in in gecco run command.
  • PyHMMER using HMM names instead of accessions, causing issues with Pfam HMMs.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.4.5

Added

  • Additional fold column to cross-validation table output. ### Changed
  • Use sequence ID instead of protein ID to extract type from cluster in gecco cv.
  • Install HMM data in pre-pressed format to make hmmsearch runs faster on short sequences.
  • gecco.orf was rewritten to extract genes from input sequences in parallel.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.5.0

Added

  • Explicit support for Python 3.9. ### Changed
  • pyhmmer is used to annotate protein sequences instead of HMMER3 binary hmmsearch.
  • HMM files are stored in binary format to speedup parsing and reduce storage size.
  • tqdm is now a training-only dependency.
  • gecco cv now requires training dependencies.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.4.4

Added

  • gecco cv loto command to run LOTO cross-validation using BGC types for stratification.
  • header keyword argument to FeatureTable.dump and ClusterTable.dump to write the table without the column header allowing to append to an existing table.
  • __getitem__ implementation for FeatureTable and ClusterTable that returns a single row or a sub-table from a table. ### Fixed
  • gecco cv command now writes results iteratively instead of holding the tables for every fold in memory. ### Changed
  • Bumped pandas training dependency to v1.0.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.4.3

Fixed

  • GenBank files being written with invalid /cds feature type. ### Changed
  • Blocked installation of Biopython v1.78 or newer as it removes Bio.Alphabet and breaks the current code.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.4.2

Fixed

  • TypeClassifier.predict_types using inverse type probabilities when given several clusters to process.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.4.0

Added

  • gecco.model.ProductType enum to model the biosynthetic class of a BGC. ### Removed
  • pandas interaction from internal data model.
  • ClusterCRF code specific to cross-validation. ### Changed
  • pandas, fisher and statsmodels dependencies are now optional.
  • gecco train command expects a cluster table in addition to the feature table to know the types of the input BGCs.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.4.1

Fixed

  • gecco run command crashing on input sequences not containing any genes.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.2.2

Changed

  • Domain and Gene can now carry qualifiers that are used when they are translated to a sequence feature. ### Added
  • InterPro names, accessions, and HMMER e-value for each annotated domain in GenBank output files.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.3.0

Changed

  • Replaced Nearest-Neighbours classifier with Random Forest to perform type prediction for candidate BGCs.
  • gecco.knn module was renamed to implementation-agnostic name gecco.types. ### Fixed
  • Extraction of domain composition taking a long time in gecco train command. ### Removed
  • --metric argument to the gecco run CLI command.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.2.1

Fixed

  • Various potential crashes in ClusterRefiner code. ### Removed
  • Uneeded feature dictionary filtering in ClusterCRF for models with Fisher Exact Test feature selection.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.2.0

Fixed

  • pandas warning about unsorted columns in gecco run. ### Removed
  • Gene.probability property, replaced by Gene.maximum_probability and Gene.average_probability properties to be explicit. ### Changed
  • Internal model now uses Pfam and Tigrfam with the top 35% features selected with Fisher's Exact Test.
  • ClusterRefiner now removes genes on Cluster edges if they do not contain any domain annotation.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.1.0

Initial release.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.1.1

Added

  • ClusterCRF.predict_probabilities to annotate a list of Gene. ### Changed
  • BGC probability is now stored at the Domain level instead of at the Gene level, independently of the feature extraction level used by the CRF.
  • ClusterKNN will use the model path provided to gecco run if any. ### Docs
  • Added this changelog file to document changes in the code.
  • Added documentation to gecco submodules missing some.
  • Included the CHANGELOG.md file to the generated docs.

- Python
Published by althonos about 5 years ago

gecco-tool - 0.0.1

Proof-of-concept.

- Python
Published by althonos about 5 years ago