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[BUG] Gene models cannot infer file format #660

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IvoTod opened this issue Jun 20, 2024 · 0 comments
Open

[BUG] Gene models cannot infer file format #660

IvoTod opened this issue Jun 20, 2024 · 0 comments
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@IvoTod
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IvoTod commented Jun 20, 2024

What happened:
When trying to load gene models from refSeq_v20240129 without specifying file format, the loader fails to infer the filetype and loading fails.

What you expected to happen:
The loader should be able to infer and load any valid file.

Minimal Complete Verifiable Example:
First download/cache hg38/gene_models/refSeq_v20240129 and then:

from dae.genomic_resources.gene_models import build_gene_models_from_file
models = build_gene_models_from_file("./ncbiRefSeq.txt.gz")
models.load()

Anything else we need to know?:
This is the output:

can't find gene model parser; inferred file formats are ['ccds', 'refseq']
can't infer gene models file format for ....

File ~/gpf/dae/dae/genomic_resources/gene_models.py:1428, in GeneModels.load(self)
   1424     if fileformat is None:
   1425         logger.error(
   1426             "can't infer gene models file format for "
   1427             "%s...", self.resource.resource_id)
-> 1428         raise ValueError("can't infer gene models file format")
   1430 parser = self._get_parser(fileformat)
   1431 if parser is None:

ValueError: can't infer gene models file format
@IvoTod IvoTod added the bug Something isn't working label Jun 20, 2024
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