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gene_regions configuration key is still used #154

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fabio-t opened this issue Jul 20, 2020 · 3 comments
Closed

gene_regions configuration key is still used #154

fabio-t opened this issue Jul 20, 2020 · 3 comments
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RGT
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0.13.1

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fabio-t commented Jul 20, 2020

gene_regions has been substituted by genes_Gencode and genes_RefSeq a long time ago (using it causes a crash, as the code does not support it).
However, data.config.user still list it - and so do the Zebrafish configuration entries.

We need to either complete the move to the new system, or add code to keep the gene_regions as an allowed configuration key.
@fabio-t fabio-t self-assigned this Jul 20, 2020
@fabio-t fabio-t added the bug label Jul 20, 2020
@fabio-t fabio-t added this to TODO in RGT via automation Jul 20, 2020
@fabio-t fabio-t added this to the 0.13.1 milestone Jul 20, 2020
fabio-t added a commit that referenced this issue Jul 20, 2020
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#154 removing references to gene_regions
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fabio-t added a commit that referenced this issue Jul 22, 2020
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#154 converted genecode/refseq duplicate entry to a single gene_regions
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fabio-t commented Jul 22, 2020

Actually ended up removing the genes_Gencode and genes_RefSeq in favour of a single genes_regions (kept the same name as in the past, for some level of retrocompatibility; but the release notes should warn the user of the need to review their data.config.user file).

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fabio-t commented Jul 23, 2020

@jovesus @lzj1769 can you have a look? I don't think it affects your tools, as genes_Gencode and genes_RefSeq were never actually used - not even in the tools.

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fabio-t commented Aug 19, 2020

fixed with #158

@fabio-t fabio-t closed this as completed Aug 19, 2020
RGT automation moved this from TODO to Done Aug 19, 2020
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