Error in gtfparse when calling vcf-expression-annotator
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- Python
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Description
I am getting the following error from the gtf library when trying to annotate my vcf with stringtie output.
$ vcf-expression-annotator -o /shared_dir/temp.annotated.vcf -s sample /shared_dir/temp.vep.vcf /shared_dir/temp.abundance.tsv stringtie transcript
Traceback (most recent call last):
File "/opt/miniconda/envs/gatk/lib/python3.6/site-packages/gtfparse/read_gtf.py", line 121, in parse_with_polars_lazy
**kwargs).lazy()
AttributeError: 'LazyFrame' object has no attribute 'lazy'
Version 2.0.1 with Python 3.6
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Research direction
Start with the traceback in gtfparse/read_gtf.py, especially parse_with_polars_lazy at line 121, and reproduce the reported vcf-expression-annotator command with gtfparse 2.0.1 on Python 3.6. Check the relevant LazyFrame API compatibility; done means the annotation command completes without the reported AttributeError.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100