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Better integrity check #343

Merged
merged 7 commits into from
Apr 16, 2024
Merged

Better integrity check #343

merged 7 commits into from
Apr 16, 2024

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MatBarba
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@MatBarba MatBarba commented Apr 15, 2024 •
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  • Separate add_error and add_errors to avoid confusion (and better type hint) Unified add_errors()
  • Return list of errors instead of numbers (homogeneity)
  • Better reports errors when 2 checks are done (e.g. Translation Fasta vs GFF with or without pseudogenes/IG genes)
  • Support for IG genes that have a CDS but have no sequence in the peptide FASTA file

MatBarba added 2 commits April 15, 2024 12:06
@MatBarba
Support IG genes with CDS but no translation in fasta
ec60c4a
@MatBarba
More homogenious errors
0045e52 
Separate add_error and add_errors because it led to confusion.
Now show a better tally of errors
@MatBarba MatBarba requested a review from Dishalodha April 15, 2024 11:17
@MatBarba MatBarba self-assigned this Apr 15, 2024
JAlvarezJarreta
JAlvarezJarreta reviewed Apr 16, 2024
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@JAlvarezJarreta JAlvarezJarreta left a comment •
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Simple changes, although I have a couple of comments/suggestions:

src/python/ensembl/io/genomio/manifest/check_integrity.py Outdated Show resolved Hide resolved
src/python/ensembl/io/genomio/manifest/check_integrity.py Outdated Show resolved Hide resolved
@MatBarba MatBarba merged commit 838df2f into main Apr 16, 2024
@MatBarba MatBarba deleted the mbarba/integrity_fix branch April 16, 2024 14:20
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@Dishalodha Dishalodha Dishalodha left review comments

@JAlvarezJarreta JAlvarezJarreta JAlvarezJarreta approved these changes

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@MatBarba @JAlvarezJarreta @Dishalodha