v2.3.4

Fix #426: Allow codon usage in Mikado prepare (#433)
Fix #431: Pin marshmallow dependency versions (#433)

Full Changelog: v.2.3.3...v2.3.4

Version 2.3.3

Bug fix release

Fixes an issue when all inputs are tagged reference and padding is activated.

Fixes #422

What's Changed

• HSP uniqueness could fail in rare cases by @ljyanesm in #423

Full Changelog: v2.3.2...v.2.3.3

Version 2.3.2

Fix issue processing empty blast tsv files.

Version 2.3.1

This release improves the performance of Mikado for dense loci when processing long read data. Also, makes Mikado compatible with SQLAlchemy 1.4.0.

Bugs fixed:

• #415
• #413
• #412

Version 2.3.0

Version 2.3.0

Fix #404: Error in extract_promoter_regions.py helper script

Fix #405: Error in remove_utrs.py helper script

Also fixes a name clashing issue in daijin's configuration object and other small bugs

Version 2.2.5

Fix for class2 in daijin pipeline

Fix #401: Cannot run Class2 in Daijin pipeline

v2.2.4

Fix the Github Action tests, moving to use only Python 3.7+ (due to AsyncIO), and updated the documentation.

Fix #385: clarified and corrected the tutorial for Daijin.
Fix #389: Mikado now can theoretically output BED12 files from Mikado prepare. This is still
Fix #395: corrected an issue in mikado prepare that left models with incorrect proteins in the input annotations. This caused mikado pick to crash during the padding procedure.
Fix #396: corrected and clarified the errors related to missing configuration files (e.g. incorrect scoring files being provided).
Fix #397: corrected a small bug in mikado prepare, when providing the input files through the CLI rather than through the configuration file.

v2.2.3: OSX

Testing Mikado also on OSX, and adding OSX to the supported OSes in Conda.

Fix #392: Mikado was having trouble with pipes in the sequence IDs (either present in the first place or added by NCBI+ when using makeblastdb -parse_seqids).

Version 2.2.2

Using TMPDIR by default when creating/reading sqlite databases, this is faster than running directly on NFS
Added an option to use /dev/shm for mikado serialise and compare

SQLA patch

Pinning sqlalchemy to <1.4.0 until sqlalchemy_utils is updated (see #388).

Moreover, solved a small bug in prepare: setting prepare.exclude_redundant to True in the configuration file had no effect. Now it is equivalent to use the -er switch on the CLI (h/t @swarbred).