From de6c1b9bc94b14346d9e2709b4749eb79eb09930 Mon Sep 17 00:00:00 2001 From: Eric Date: Mon, 16 Dec 2024 11:24:05 -0600 Subject: [PATCH 1/2] Updating versions. --- CHANGELOG.md | 2 +- staramr/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 35f0503..09738ec 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,4 +1,4 @@ -# Unreleased +# Version 0.11.0 * Updated the Resfinder database to use the 2024-08-06 release. * Updated the Pointfinder database to use the 2024-08-08 release. diff --git a/staramr/__init__.py b/staramr/__init__.py index fe2ef9e..f323a57 100644 --- a/staramr/__init__.py +++ b/staramr/__init__.py @@ -1 +1 @@ -__version__ = '0.11.0.dev0' +__version__ = '0.11.0' From 2dd00853b909a9a9e90ed9d088e4fceba60e021b Mon Sep 17 00:00:00 2001 From: Eric Date: Mon, 16 Dec 2024 13:10:03 -0600 Subject: [PATCH 2/2] acrB 171 -> acrB 717 --- CHANGELOG.md | 1 - staramr/databases/resistance/data/ARG_drug_key_pointfinder.tsv | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 09738ec..ed37717 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,7 +5,6 @@ * The Resfinder and Pointfinder databases now use FASTA record IDs with accession numbers (ex: `pmrA` -> `pmrA_1_CP055130.1`). StarAMR has been updated to support this, but database backwards compatibility is unlikely. * The `genes_to_exclude` is affected by the above change and must now use gene IDs that exactly match the new FASTA record IDs with accession IDs. * Removed ARG drug key entries with "None" or missing resistance. -* The ARG drug key for salmonella acrB 717 has changed to acrB 171. # Version 0.10.0 diff --git a/staramr/databases/resistance/data/ARG_drug_key_pointfinder.tsv b/staramr/databases/resistance/data/ARG_drug_key_pointfinder.tsv index 9d31ef2..3f8565c 100644 --- a/staramr/databases/resistance/data/ARG_drug_key_pointfinder.tsv +++ b/staramr/databases/resistance/data/ARG_drug_key_pointfinder.tsv @@ -47,7 +47,7 @@ salmonella parE 514 ciprofloxacin I/R,nalidixic acid salmonella parE 521 ciprofloxacin I/R,nalidixic acid salmonella 16S_rrsD 1065 spectinomycin salmonella 16S_rrsD 1192 spectinomycin -salmonella acrB 171 azithromycin +salmonella acrB 717 azithromycin escherichia_coli gyrA 51 ciprofloxacin I/R,nalidixic acid escherichia_coli gyrA 67 ciprofloxacin I/R,nalidixic acid escherichia_coli gyrA 81 ciprofloxacin I/R,nalidixic acid