macrel - v1.5.0

Add support for local querying of the AMPSphere

Full ChangeLog:

• Add support for local searching
• Slightly change output format for AMPSphere matching
• Add --verbose and --quiet flags

- Python
Published by luispedro over 1 year ago

macrel - Version 1.4.0

Adds query-ampsphere command to query the AMPsphere database (described in Santos-Júnior et al., 2024).

- Python
Published by luispedro over 1 year ago

macrel - Version 1.2.0

Use pyrodigal instead of a modified version of prodigal.

- Python
Published by luispedro almost 4 years ago

macrel - Version 1.1.0

• 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:

- Python
Published by luispedro almost 4 years ago

macrel - Version 1.0.1

Bugfix release. Fixes bug when "peptides" with 2 amino acids are present (it used to crash)

- Python
Published by luispedro over 4 years ago

macrel - Version 1.0.0

Version 1.0 to coincide with paper publication DOI:10.7717/peerj.10555.

The big user-visible change is adding README.md files to the output directories documenting the output files

- Python
Published by luispedro about 5 years ago

macrel - Version 0.6.1

Makes atomicwrites into an optional dependency: atomicwrites causes issues, especially on Mac OSX

- Python
Published by luispedro over 5 years ago

macrel - Version 0.6.0

A series of user-experience improvements:

• Add --log-append flag
• Add --log-file argument
• Add usage example in command line help message
• Use atomic writing for output to avoid partial results

- Python
Published by luispedro over 5 years ago

macrel - Version 0.5.0

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

- Python
Published by luispedro almost 6 years ago

macrel - Version 0.4.0

Biggest change is the use of a new feature computation where initial Methionines are removed for robustness.

- Python
Published by luispedro almost 6 years ago

macrel - Release 0.3.1

Fixes an issue with v0.3 which used non-Python 2 compatible syntax.

- Python
Published by luispedro about 6 years ago

macrel - Version 0.3

• Added get-examples command
• Added get-smorfs command
• Updated training sets: results should be slightly better
• Converted to scikit-learn
• Fix license (must be GPL because of Peptides)
• Code is slightly faster at feature computation

- Python
Published by luispedro about 6 years ago

macrel - Version 0.2

Python version implementing the process described in the preprint.

- Python
Published by luispedro about 6 years ago

macrel - Version 0.1

Bash version

This is the version tested in the preprint

- Python
Published by luispedro about 6 years ago