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Seq_region lrg support #241

Merged
merged 3 commits into from
Jun 19, 2024
Merged

Seq_region lrg support #241

merged 3 commits into from
Jun 19, 2024

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MatBarba
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@MatBarba MatBarba commented Dec 6, 2023

Not sure how to handle this properly: the human core db contains a coord_system_level named lrg (not SO terms).

This PR is to make the validation pass for that genome. An alternative would be to add a list of coord_system_level that we would not dump in the seq_region dumper, but that'd mean we don't dump everything.

@MatBarba MatBarba changed the title Mbarba/seq region lrg Seq_region lrg support Dec 6, 2023
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@JAlvarezJarreta JAlvarezJarreta left a comment

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LRGs are quite tricky (the Perl codebase is full with conditionals for this data) and definitely not free of headaches. I agree we should be avoiding these for now. Furthermore, VEuPathDB always claims HostDB species should be basic pointers to better resources such as Ensembl, so this change also aligns with that decision. 👍

@MatBarba
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MatBarba commented Dec 7, 2023

LRGs are quite tricky (the Perl codebase is full with conditionals for this data) and definitely not free of headaches. I agree we should be avoiding these for now. Furthermore, VEuPathDB always claims HostDB species should be basic pointers to better resources such as Ensembl, so this change also aligns with that decision. 👍

This PR does dump the lrg sequences, so do I need to make a different PR where the code explicitly exclude them from the dumps?

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Sorry, I completely misread the intention of this PR 🤦‍♂️ It's ok either way, so if we are currently dumping them without issues, happy with that. 👍

@MatBarba MatBarba closed this Dec 11, 2023
@MatBarba MatBarba reopened this Jun 18, 2024
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Reopening because I don't think it would hurt to have this and it's very simple

@JAlvarezJarreta JAlvarezJarreta merged commit a8b00f6 into main Jun 19, 2024
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@JAlvarezJarreta JAlvarezJarreta deleted the mbarba/seq_region_lrg branch June 19, 2024 11:29
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2 participants