Push forward

Improvements:

• #15 BLAST now used to determine whether we are looking at a tandem duplication or not
• #16 Improved BLAST loading (to be tested)
• #23 (Sorted output)
• #24 (Check input is properly sorted)

Bug fixes:

• #20 Correctness of retained introns

The day after

Changelog:

• redesigned BLAST HSP checks before splitting; now we should be able to call a fusion even when there are hits in common. Parameter: min_overlap_duplication in the config.
• Redesigned the retained_intron method, now it is quite better and cleaner.
• switched to the example region in Chr5 for the sample data. Kept old files anyway.
• Now the AS events have a ccode tag attached (compared to the primary transcript)
• BF, very serious, on scores assigned to transcripts in loci with only 1 sequence.
• BF for primary transcripts not correctly annotated.
• BF for redundancy in AS events retrieval.
• GFF output now is completely GT-validated.
• Added logs for the serialisation step.

The great polish

The whole Mikado has been revisited and polished using pylint as a guide.

Notable feature additions:

• added an XML merger (mikado.py util merge_blast)
• written an Abstract Class that now underlies both GtfLine and GffLine, leading to far less code duplication
• simplified most of the methods and reduced the size of most functions, e.g. in the compare procedure.
• added and tested phase calculation for CDS features
• created a new module for log utilities (currently a stub)
• added the possibility of specifying "good" class codes for alternative splicing events
• database names changed and simplified

WARNING: databases serialised with earlier versions of Mikado are NOT COMPATIBLE with 0.8.7 onward.

It seems I've been running in the wrong direction

Changes since 0.8.4:

• Added exonic precision/recall/F1 to compare
• Solved a serious bug that implied the setting of strand to + for all transcripts.
• Corrected "mikado.py util grep -v " for GFFs
• Added option "min_orf_length" to determine at runtime the minimal ORF length to be loaded for transcripts.

Back to school

Bug fix release:

• Fixed issue whereby superloci where not splitted correctly after ORF information loading
• Modified GFF/GTF so that the "parent" property is faster
• Minor BFs, such as now mikado.py without arguments will not crash
• Fixed bug of incorrect ORF loading when two ORFs are intersecting by exactly 1 bp

Summertime

Frozen status before 14/08.