From d802647572f598b4d0008c0041bd88d0cd871c70 Mon Sep 17 00:00:00 2001 From: Vedanth Ramji Date: Sun, 2 Jun 2024 08:29:18 -0400 Subject: [PATCH 1/2] DOC Update changelog with adding missing ARO mappings to manual curation and case-independent inputs on command-line Note: Still waiting to finish adding missing manual curations for NCBI --- CHANGELOG.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 98cd850..7943a66 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,13 @@ ## 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 +- Accept inputs in case-independent way on command-line (by @sebastianLedzianowski) ## 0.3.0 - 27 April 2024 From 9f8f708b936919e257c880e00a97dcfe04abd4f6 Mon Sep 17 00:00:00 2001 From: Vedanth Ramji Date: Tue, 4 Jun 2024 13:15:17 -0400 Subject: [PATCH 2/2] DOC explain missing NCBI manual curation & add manual curation additions to changelog NCBI also has stress response genes and virulence genes not covered by CARD. This is the reason for the missing mappings in NCBI curation. --- CHANGELOG.md | 2 ++ argnorm/data/manual_curation/README.md | 6 +++++- 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7943a66..05351d2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ - 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 diff --git a/argnorm/data/manual_curation/README.md b/argnorm/data/manual_curation/README.md index cc7f096..9a87a2c 100644 --- a/argnorm/data/manual_curation/README.md +++ b/argnorm/data/manual_curation/README.md @@ -18,4 +18,8 @@ 9) aac(3)-I_1_AJ877225 - 9 genes in reverse complement form also present. -- RC genes were manually curated \ No newline at end of file +- 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. \ No newline at end of file