-i option seems to have no effect on filtering [intronIC v2.4.2]

[arabec]

Hi,

First of all, thank you for this very useful tool.

I seem to have encountered an issue with the -i option. I ran intronIC on human annotations (EnSEMBL release 110 GTF, GRCh38), both with and without this option enabled, but obtained identical results in both cases.

Below are the commands I used, along with the filtering section of the logs. From what I can see, introns located in alternative isoforms still appear to be filtered out even when using the -i option.

intronIC classify -g /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa -a /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.110.gtf -n Homo_sapiens -p 4

Total genes: 62,754, introns generated: 1,396,783
Intron Filtering Summary:
┌────────────────────────────┬────────────┬────────────┐
│ Category │ Included │ Excluded │
├────────────────────────────┼────────────┼────────────┤
│ Duplicates │ 0 │ 994,237 │
│ Too short │ 0 │ 99 │
│ Ambiguous bases │ 0 │ 0 │
│ Non-canonical │ 4,522 │ 0 │
│ Overlapping │ 0 │ 0 │
│ Alternative isoform │ 0 │ 171,225 │
├────────────────────────────┼────────────┼────────────┤
│ Total excluded │ │ 1,165,561 │
│ Retained for scoring │ │ 230,655 │
└────────────────────────────┴────────────┴────────────┘

intronIC classify -g /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa -a /mnt/data/arabec/refs/GRCh38/Homo_sapiens.GRCh38.110.gtf -n Homo_sapiens -i -p 4

Total genes: 62,754, introns generated: 1,396,783
Intron Filtering Summary:
┌────────────────────────────┬────────────┬────────────┐
│ Category │ Included │ Excluded │
├────────────────────────────┼────────────┼────────────┤
│ Duplicates │ 0 │ 994,237 │
│ Too short │ 0 │ 99 │
│ Ambiguous bases │ 0 │ 0 │
│ Non-canonical │ 4,522 │ 0 │
│ Overlapping │ 0 │ 0 │
│ Alternative isoform │ 0 │ 171,225 │
├────────────────────────────┼────────────┼────────────┤
│ Total excluded │ │ 1,165,561 │
│ Retained for scoring │ │ 230,655 │
└────────────────────────────┴────────────┴────────────┘

Could you please have a look at this behavior?

Thank you very much for your help.

Best regards,
Alexia

Conda environment details:
intronIC version: 2.4.2
Python version: 3.11.15

[glarue]

Hi @arabec thanks for raising this - definitely a bug from the v1 --> v2 move.

I've backported a fix to the new v2.4.3 release; please let me know if it's still giving you problems.

Also if you're planning on using it for extensive work in the near future, I'm currently finalizing a new release that will incorporate some additional multi-species training data and a few other improvements that might be worth waiting for depending on your use-case.

[arabec]

Hi,

Thank you for your quick response. The solution works perfectly.
I’ll wait a bit as suggested. Thanks again for the information.

Best regards,
Alexia