Find_AS_Events.py error

[kir1to455]

Hi,
Thank you for developing TEQUILA-seq !
I have encountered some problems when I use Find_AS_Events.py to define alternative splicing events.
Here is my code:
python ${TEQUILA_Dir}/Find_AS_Events.py -i ${Output_Dir}/samples_N2_R0_updated.gtf -r ${IndexDir}/gencode.vM33.basic.annotation.gtf -o ${Output_Dir}/DirectRNA_AS_envents.tsv
Here is the error:

'ENSMUSG00000002059.19' exists in both input transcripts.gtf and GENCODE.gtf.

Could you give me some advice?
Best wishes,
Kiritio

[kir1to455]

My ESPRESSO version is 1.3.2.

[kir1to455]

I think I've found the problem, Find_AS_Events.py line 284 does not take into account the situation where this gene does not have a canonical transcript.
I added a line above.
if gene_id in canonDict:
And added a line below.
else:
output.append([row['chr'], row['strand'], gene_id, row['transcript_id'], 'NA', 'NA', 'NA', 'intergenic_transcript'])
It's working properly now.

[EricKutschera]

It looks like the Ensembl canonical transcript for ENSMUSG00000002059.19 is not a "basic" transcript. The canonical transcript is in gencode.vM33.annotation.gtf, but not gencode.vM33.basic.annotation.gtf. I was able to reproduce the error on another dataset by using the gencode basic gtf

Here's a PR based on the code change you suggested. With that change there is no error even with the gencode basic annotation: #2