- Stats is now much faster and lighter, as objects are discarded upon analysis, not kept around for the whole run duration - Pick now preferentially outputs only one ORF per transcript, behaviour regulated by pick/output_format/report_all_orfs - BugFix for the detection of fragments during pick
0.23.0
New features:
- Added a converter for (GTF <=> GFF3) > BED12 conversions in mikado.py util convert - Now it is possible to provide a predefined malus/bonus to transcripts according to their sources using the following syntax in the configuration file:
It is generally *not* advised to use such an option unless the user really wants to emphasize or penalise a particular set of transcripts, eg. those coming from PacBio data.
0.22.0
Transitioned the XML parser to the experimental Bio.SearchIO module, which uses internally C-level APIs and is therefore twice as fast than the canonical implementation. This required some rewriting at the class level in Mikado and a cloning of the original class to make it a proper iterative class. Moreover, now requirements for the scoring can accept also eg boolean values.
0.21.0
Major changes for this release:
- Trim is now functioning - ORFs from transdecoder are treated correctly - even truncated and internal ones. No more faux UTRs! - Changes in the DB structure to accomodate the ORF information - note, this means that the databases have to be regenerated