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DOC Update changelog with adding missing manual curtion & case-independent inputs on command-line #49

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Jun 5, 2024
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DOC Update changelog with adding missing manual curtion & case-independent inputs on command-line #49

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DOC Update changelog with adding missing ARO mappings to manual curat…
Vedanth-Ramji Jun 2, 2024
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DOC explain missing NCBI manual curation & add manual curation additi…
Vedanth-Ramji Jun 4, 2024
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9 changes: 9 additions & 0 deletions CHANGELOG.md
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## Unreleased

- Bundle a specific version of ARO with the package instead of downloading it from the internet (ensures reproducibility)
- Add ADD missing ARO mappings to manual curation. A few ARO mappings were missing in the manual curation and they have been added.

Additions:
- argannot_curation: (Phe)cpt_strepv:U09991:AAB36569:1412-1948:537 -> ARO: 3000249
- megares_curation: MEG_2114 -> ARO: 3000249, MEG_2430 -> ARO: 3000016, MEG_985 -> ARO: 3000229, MEG_2865 -> ARO:3000387, MEG_7974 -> ARO:3000076
- sarg_curation: AM180355.1.gene2260.p01 -> ARO: 3000250
- resfinder_curation: dldHA2X_1_AL939117 -> ARO:3003970, grdA_1_QJX10702 -> ARO:3007382, EstDL136_1_JN242251 -> ARO:3000387
- resfinderfg_curation: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase|KF629588.1|pediatric_fecal_sample|CYC -> ARO:3003970
- Accept inputs in case-independent way on command-line (by @sebastianLedzianowski)

## 0.3.0 - 27 April 2024

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6 changes: 5 additions & 1 deletion argnorm/data/manual_curation/README.md
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9) aac(3)-I_1_AJ877225

- 9 genes in reverse complement form also present.
- RC genes were manually curated
- RC genes were manually curated

# NCBI Notes

NCBI also has stress response genes and virulence genes not covered by CARD. This is the reason for the missing mappings in NCBI curation.
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