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Recent Releases of Binette

Binette - Binette v1.1.2

What's Changed

  • Reproductible results: Bins are now sorted to ensure consistent IDs across runs. PR https://github.com/genotoul-bioinfo/Binette/pull/57 - Should fix #54
  • Faster duplicate contig check: Improved the check for duplicate contigs in input bins using Counter. PR https://github.com/genotoul-bioinfo/Binette/pull/64 - Partially fixes https://github.com/genotoul-bioinfo/Binette/issues/62
  • Avoid pyfastx-related issues: Replaced the use of pyfastx index with a custom buffered method to avoid memory issues to avoid the corrupted size vs. prev_size error from pyfastx. PR https://github.com/genotoul-bioinfo/Binette/pull/65 - Fixes #58

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.1.1...v1.1.2

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy 8 months ago

Binette - Binette v1.1.1

What's Changed

  • Fix intermittent error caused by how Binette handles the pyfastx index. (Issue #49, PR #52).

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.1.0...v1.1.1

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy 11 months ago

Binette - Binette v1.1.0

What's Changed

  • Updated Binette dependencies to align with CheckM2 v1.1.0 (#44). Binette now runs on Python 3.12 (previously 3.8) and uses Diamond >=2.1 (previously 2.0.4), fixing #13.
  • Changed license from MIT to GNU GPL to comply with CheckM2's licensing terms (#44).
  • Fixed pyfastx index setup for the contig FASTA file when writing final bins (#45).

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.5...v1.1.0

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy 12 months ago

Binette - Binette v1.0.5

What's Changed

  • Fix an error when writing input bin metrics: Resolved an issue where identical input bins from different bin sets were not properly dereplicated when writing metrics, producing an unscored bin error. The dereplicated bins are now exclusively used, ensuring accurate tracking and avoiding such errors. (Reported in issues #34 and #39, fixed in PR #36)

- Fix incorrect input proteins management: When dealing with input protein file, Binette was not expecting proteins from unbinned contigs. The input protein file is now filtered to exclude genes from unbinned contigs, ensuring only protein data from contigs within the input bins is used. (See PR #37, reported in issue #35)

Additional Updates

  • Temporary files in <outdir>/temporary_files/ are now compressed, optimizing storage. (PR #37)
  • The pyfastx index for contig files is stored in <outdir>/temporary_files/ instead of alongside the assembly file, ensuring cleaner directory management. (PR #37)

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.4...v1.0.5

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy about 1 year ago

Binette - v1.0.4

What's Changed

  • Possibility to provide precomputed gene sequences: You can now use the --genes argument to provide precomputed protein sequences, bypassing the gene-calling step. (See PR #31, requested in issue #30, documentation)
  • Code formatting with Black: Added the Black formatter to ensure a consistent and clean codebase. (PR #32)

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.3...v1.0.4

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy about 1 year ago

Binette - Binette v1.0.3

What's Changed

This release contains no specific changes to the codebase, but includes final changes to the JOSS paper (PR #26) and also updates and fixes minor details in the tutorial section of the documentation (PR #27 & #28).

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.2...v1.0.3

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy over 1 year ago

Binette - Binette v1.0.2

What's Changed

  • New Tutorial: Added a tutorial that walks through how to use Binette with real data. (from PR #23 )

  • Better Bin Set Naming: Improved how bin set names are inferred from input directories or tables. (from PR #25)

  • New Output Files:

    • The directory input_bins_quality_reports is now created in the output repository, which stores quality reports for the initial bin sets. This helps compare how much Binette improves the bins compare to the input bins. (from PR #25)

  • Refactoring:

    • Cleaned up some typing issues flagged by Pylance.
    • Switched from os.path to pathlib for better path handling.

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.1...v1.0.2

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy over 1 year ago

Binette - v1.0.1

What's Changed

  • Improve error management to provide clear message when the contigs input and bin tables do not match. (PR #12, issue #11)
  • FASTA file selection in the bin directory is now based on file extensions. Previously, all files in the directory were expected to be bins in FASTA format. The extensions to search for can be specified with --fasta_extensions. By default, fasta, .fna, and .fa are considered. (Added in PR #16, issue #14)
  • Added more unit tests to increase test coverage.

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v1.0.0...v1.0.1

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy over 1 year ago

Binette - Binette v1.0.0

First official release of Binette. :rocket:

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v0.1.7...1.0.0

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy about 2 years ago

Binette - Binette v0.1.7

  • Added unit tests and coverage (#4).
  • Introduced documentation hosted on Read the Docs: https://binette.readthedocs.io (#5).
  • Implemented a workflow to automate the publication of Binette on PyPI (#5).

Full Changelog: https://github.com/genotoul-bioinfo/Binette/compare/v0.1.6...v0.1.7

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy about 2 years ago

Binette - Binette v0.1.6

A minor change in how to retrieve binette version in binette.py to fix error in bioconda recipe: https://github.com/bioconda/bioconda-recipes/pull/42477

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy over 2 years ago

Binette - Add usage and fix minor issue in N50 and length of bins in final bin table

This minor release includes the addition of a comprehensive usage section in the README.md, which aims to facilitate the usage of Binette (#2 ). Additionally, it addresses a minor issue where the N50 and length values of the bin reported in the final bin table were incorrectly set to None.

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy over 2 years ago

Binette - Improve install

Minor release - Simplify install of checkm2 using conda. - Fix import bug - update Readme accordingly

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy almost 3 years ago

Binette - Binette v0.1.3

Add some github actions to check binette installation. Follow checkm2 v1.0.2 release.

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy almost 3 years ago

Binette - Binette v0.1.2

Added the argument --checkm2_db to be able to provide the checkm2 database as a cli argument of Binette. It follows the release of checkm2 version v1.0.1

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy almost 3 years ago

Binette - First pre release of Binette

Scientific Software - Peer-reviewed - Python
Published by JeanMainguy about 3 years ago