This release is mainly focused on two aims: integration with Dagger, and the possibility of performing a good self-comparison with mikado.py compare.
Detailed changes for the release:
- scoring files are now inside a proper subfolder, and can be copied during configuration, for user modification
- the configuration process has now been widely rehauled, together with the configuration files, to make Mikado compatible with DAGGER
- Introduced a functioning deep copy method for gene objects
- Now redundant adding of exons into a transcript object will not throw an exception but will be silently ignored
- Mikado parsers now support GZIPped and BZIPped files, through python-magic
- added the possibility of specifying which subset of input assemblies are strand-specific during the preparation step
- configure and prepare now accept a tab-separated text file (format: , ) as input
- compare now can perform two types of self-analysis:
- "internal", which outputs only a tmap file and performs a comparison all-vs-all within each multi-isoform gene locus
- "self", in which each transcript is analysed as it would during a normal run, but removing itself from the reference.
- Now serialise can accept FASTA references, pyFaidx is used to recover the correct FAI
- pick and configure can now specify the mode of action (nosplit, split, stringent, lenient, permissive) by CL instead of having to modify the configuration file
- cleaned up the sample_data directory, plus now the configuration file is created on the spot by Snakemake (ensuring compatibility with the latest version)