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@lucventurini lucventurini released this 15 Oct 13:48
· 514 commits to master since this release
1.3beta
adc5de0

[Beta, the finalised version will be released soon]

One of the major highlights of this release is the completion of the "padding" functionality.
Briefly, if instructed to do so, now Mikado will be able to uniform the ends of transcripts within a single locus (similar to what was done for the last Arabidopsis thaliana annotation release).
The behaviour is controlled by the "pad" boolean switch, and by the "ts_max_splices" and "ts_distance" parameters under "pick".

Bugfixes and improvements:

  • Fixed a bug which caused some loci to crash at the last part of the picking stage
  • Now coding and non-coding transcripts will be in different loci.
  • Mikado prepare now can accept models that lack any exon features but still have valid CDS/UTR features
  • Fixed #34: now Mikado can specify a valid codon table among those provided by NCBI through BioPython. The default is "0", ie the Standard table but with only the canonical "ATG" being accepted as valid start codon.
  • Fixed #123: now add_transcript_to_feature.gtf automatically splits chimeric transcripts and corrects mistakes related the intron size.
  • Fixed #126: now reversing the strand of a model will cause its CDS to be stripped.
  • Fixed #127: previously, Mikado prepare only considered cDNA coordinates when determining the redundancy of two models. In some edge cases, two models could be identical but have a different ORF called. Now Mikado will also consider the CDS before deciding whether to discard a model as redundant.
  • #129: Mikado is now capable of correctly padding the transcripts so to uniform their ends in a single locus. This will also have the effect of trying to enlarge the ORF of a transcript if it is truncated to begin with.
  • #130: it is now possible to specify a different metric inside the "filter" section of scoring.
  • #131: in rare instances, Mikado could have missed loci if they were lost between the sublocus and monosublocus stages. Now Mikado implements a basic backtracking recursive algorithm that should ensure no locus is missed.
  • #132: Mikado will now evaluate the CDS of transcripts during Mikado prepare.
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