Error: 'NoneType' object has no attribute 'noncanonical'

[alejandrogzi]

Pipeline Steps
├── ▶ Load and extract introns
├── ○ Score introns with PWMs
├── ○ Normalize scores
├── ○ Train and apply classifier
└── ○ Write output files
ℹ Loading genome: HLeonSpe2A.fa
[12:54:54] ℹ Loaded 305 sequences into memory
ℹ Reading BED file: single.bed
ℹ Extracting sequences from genome
[12:55:06] ✗ Pipeline failed: 'NoneType' object has no attribute 'noncanonical'

Error: 'NoneType' object has no attribute 'noncanonical'

intronIC --version
intronIC 2.1.4

[alejandrogzi]

That is coming from using a BED12 as --bed. The docs say 'intron coordinates'. I would assume that means BED3/BED6 with specific coords and not extract intron coordinates from BED12, right?

[glarue]

Hey @alejandrogzi thanks for raising this—looks like a regression from the v1 to v2 move. Should be fixed in v2.1.5, which I just pushed (2e68a3c). If you can test on your end and report back that would be great.

[ReverendCasy]

Hello @glarue ,
Thank you for the fix. I confirm that 2.1.5 works fine with BED6 intron files, contrary to 2.0.0-2.1.4 releases. Are you going to upload this release to PyPI as well?
@alejandrogzi thank you for raising the issue!

[glarue]

@ReverendCasy yes, there's now an automatic release-based trigger to push to PyPI as well so it should already be there!