v1.5.0

What's Changed

• Modernized packaging with pyproject.toml (PEP 517/518 compliant)
• Dropped support for Python 3.7 and 3.8 (end of life)
• Added support for Python 3.13
• Added type hints throughout the codebase
• Default to sans-serif fonts (Arial) for plotting
• Updated copyright to 2020-2026

Full Changelog: v1.4.0...v1.5.0

v1.4.0

What's Changed

• Add new meta_min_reads CLI param by @pinin4fjords in #155
• Fixing linter errors by @andrewdavidsmith in #158

New Contributors

• @pinin4fjords made their first contribution in #155
• @andrewdavidsmith made their first contribution in #158

Full Changelog: v1.3.3...v1.4.0

v1.3.3

• Print start codons when preparing orfs
• Fix for custom start codons

Full Changelog: v1.3.2...v1.3.3

v1.3.2

• Better support for extracting sequences from non-conventional GTFs
• Support --protein flag for extracting protein sequences

v1.3.1

• Detecting uniquely mapping reads now raises a warning instead of aborting. We expect the user to ensure all reads in the bam are uniquely mapping unless it was produced for aligners that support either the NH or standard uniquely mapping flags (See common.py for a list of flags).
• Clean setup.py to improve classifiers

v1.3.0

Bug Fixes:

• A small bug fix in metagene.py where the first annotated CDS was being skipped

Improvements:

• Silenced progress bars after they are complete
• More informative progress messages

v1.2.0

• Added additional flags for filtering:

  • --min_valid_codons_ratio (default=0): Minimum ratio of codons with non-zero reads to total codons for
    determining active translation
  • --min_reads_per_codon (default=0): Minimum number of reads per codon for determining active translation
  • --min_read_density (default=0.0): Minimum read density (total_reads/length) over an ORF total codons for determining active translation

• Added a new command-line argument to learn dataset-specific parameters from Ribo-seq and RNA-seq bams learn-cutoff

• Travis based CI testing

v1.1.0

• Allow specifying custom phase score cutoffs
• Added documentation for species-specific cutoffs
• Helper functions for determining best cutoff given golden datasets

First pypi release

• ribotricer is now pypi compatible!

First stable public release of ribotricer

v1.0.0

Bump version: 1.0.0-dev0 → 1.0.0