What's new? (History)
Version 1.3.0
Released 5 December 2023
- Adds density estimates to output
- Adds compatibility with Pyrodigal ≥3
Version 1.2.0
Released May 9 2022
- Adopt pyrodigal v.0.7.3 to predict genes
- Implement a hybrid gene prediction system: training mode for contigs > 100kbp and use pre-trained models for smaller contigs
Bugfixes
- Fix the README files generation by the output type
Version 1.1.0
Released November 8 2021
- Add support for bzip2 and xz compressed FASTA files
- Eliminate R dependency
- Include more extensive testing
- New feature computation code (Python implementation) made macrel about 3.5 times faster than before:
Time \ Code | version 1.0.1 | version 1.1.0 |
---|---|---|
Real | 60m 44.380s | 17m 15.313s |
User | 33m 37.604s | 9m 38.034s |
System | 0m 16.076s | 0m 6.270s |
Bugfixes
- Fix abundance/reads modes when single-ended reads were used
Version 1.0.1
Released September 2 2021
Bugfixes
- No longer crash on very short peptides (1 or 2 amino acids)
Version 1.0.0
Released December 21 2020
User-visible improvements
- Add README.md files to the output directories documenting the output files
Version 0.6.1
Released October 29 2020
User-visible improvements
- Atomicwrites is now an optional dependency. This implies a loss of functionality if not available (file writing is no longer atomic), but the atomicwrites dependency caused issues (especially on Mac)
Version 0.6.0
Released October 10 2020
User-visible improvements
- Add
--log-file
and--log-append
command line arguments - Add usage example in command line help message
- Output is now written atomically (i.e., no partial files)
Version 0.5.0
Released May 11 2020
User visible changes
- Fix bug with Prodigal by changing internal parameters. Although this is a bugfix, it will also change the results in some cases.
- Output table now includes the version on the header
Bugfixes
- Fix bug with using
--force
and existing directories
Version 0.4.0
Released March 16 2020
User-visible improvements
-
Add
--keep-negatives
flag -
Add warning for longer sequences
-
Remove Methionine from N-terminus
Bugfixes
- Fix for when no smORFs are present
Version 0.3.1
Released January 24th 2020
Bugfixes
- Fix for Python 2.7
Version 0.3.0
Released January 24th 2020
User-visible improvements
- Add
get-examples
command - Add
get-smorfs
command
Internal improvements
- Convert to scikit-learn
- Updated training sets
- Fix license (must be GPL because of Peptides)
Version 0.2.0
Released January 14th 2020
- Complete release