DEXSeq prepare annotation script throws “object has no attribute ‘next'” for Ensemble GTFs

@24764cda

Last seen 23 hours ago

United States

Hi there,

I am trying to run the dexseq_prepare_annotation.py script and the code keeps failing after parsing the first line of the gtf. Specifically, the code is failing at the first step where exons and their respective gene and transcript IDs are placed into a GenomicArrayOfSets. I’ve tried this with three different GTFs from Ensembl and all three lead to the same error.

Traceback (most recent call last):
File “/Library/Frameworks/R.framework/Versions/4.0/Resources/library/DEXSeq/python_scripts/dexseq_prepare_annotation.py”, line 56, in <module>
exons[f.iv] += ( f.attr[‘gene_id’], f.attr[‘transcript_id’] )
File “src/HTSeq/_HTSeq.pyx”, line 451, in HTSeq._HTSeq.ChromVector.__iadd__
File “src/HTSeq/_HTSeq.pyx”, line 464, in HTSeq._HTSeq.ChromVector.apply
File “…miniconda3/lib/python3.9/site-packages/HTSeq/_HTSeq_internal.py”, line 33, in ChromVector_steps
for start, stop, value in cv.array[cv.iv.start:cv.iv.end].get_steps():
File “…miniconda3/lib/python3.9/site-packages/HTSeq/StepVector.py”, line 410, in get_steps
prevval = startvals.next().second
AttributeError: ‘_StepVector_Iterator_obj’ object has no attribute ‘next’

Python version = 3.9.5
Htseq version = 0.13.5
DEXSeq version = DEXSeq_1.36.0