intronIC v1.5.2

BUGFIX: intronIC now correctly handles cases where, using BED-format input, putatively-misannotated U12-type introns are identified and have their coordinates adjusted. Previously, this triggered a GTF/GFF-centric subroutine to adjust annotated exon/CDS coordinates based on the new intron coordinates, which threw an error when running with BED input.

intronIC v1.5.1

intronIC v1.5.1

• BUGFIX: BED output start coordinates are now (correctly) 0-indexed rather than 1-indexed (thanks @MichaelHiller)
• New arg --no_nc_ss_adjustment disables the default heuristic for detecting putatively-misannotated U12-type introns by the presence of a strong U12-like 5′SS near the annotated start site of non-canonical introns.

intronIC v1.4.0

Include networkx as a dependency in setup.cfg, where it should have been all along.

intronIC v1.3.7

Fix annoying issues with generating a version number under different installation scenarios.

intronIC v1.3.6

• Deal with edge-case issue where a gene feature has children
  exon/CDS features in a direct parent-child relationship.
  Previously, this would bypass the recursive search for introns used
  by get_introns() due to an early exit, resulting in preferential
  inclusion of introns whose Parent attribute was the gene itself
  rather than a child transcript.
• Remove old code/fix whitespace
• Update __version__ paradigm
• Remove Physarum-specific branch-point PWM code

intronIC v1.3.2

Misc. minor changes not affecting functionality.

Switch to limiting master (soon to be main) to point releases, with development code contained to dev.

intronIC v1.3.0

• Changes default scoring behavior to include all (5', BPS and 3') regions, instead of the previous default of just 5' and BPS. The 3' region typically contains less differentiation between U2- and U12-type introns, but may help reduce FP and FN classifier calls in edge cases. Of course, it's also possible that it could also introduce FPs and/or FNs, although in my experience using all three seems to be more conservative than not.
• Misc. minor internal changes.

intronIC v1.2.0

intronIC v1.2.0

• Fix GridSearchCV regression with newer versions of scikit-learn (>v0.22) (see issue #1)
• Due to scikit-learn's inversion of a default flag in GridSearchCV, intronIC must now require scikit-learn to be at least v0.22
• This fix breaks compatibility with scikit-learn versions <v0.22

intronIC v1.1.1

intronIC v1.1.1

• Replace parent-child hierarchical clustering of annotation features with simpler, directed graph-based approach
• Fix occasional issues where parent genes of CDS/exon features weren't correctly identified

intronIC v1.1.0

A number of changes to the underlying data in this release - the default PWMs have been changed to a slightly less-stringent set, which should leave most results relatively unchanged and deals with some edge-cases where the original PWMs were overly penalizing for certain base positions due to being built from low-N samples. Other changes include:

• Default 3'SS region shortened to [-6, 4]
• By default, the human U2-type BPS PWM is used instead of the on-the-fly version. A per-run PWM can be generated using --generate_u2_bps_pwm
• z-scores in the output have been adjusted to correspond to the entire dataset (previously, they were based on the training set only)
• Non-canonical introns by default now use whatever PWM is closest to their terminal dinucleotides if one is obvious (e.g. for AT-TC introns, this would be the AT-AC PWM; for AT-AG introns, GT-AG and AT-AC are equally close in terms of edit distance). Otherwise, the terminal dinucleotides will be ignored and the best PWM will be selected based on the geometric mean of the component scores from each PWM. This can be reverted to the old behavior using --no_ignore_nc_dnts