From fa7ffd26630d35407018a49e97becf43a83f19e3 Mon Sep 17 00:00:00 2001 From: Jake Beal Date: Fri, 31 Mar 2023 15:07:21 -0500 Subject: [PATCH 1/2] NCBI's taxonomy has changed Proteobacteria to Pseudomonadota, which affects all tests involving the GenBank import of an E. coli sequence --- scripts/test/test_files/NCBI_GenBank_imports.gb | 2 +- scripts/test/test_files/distribution/distribution.nt | 2 +- scripts/test/test_files/imports/imports_test_ncbi.gb | 2 +- scripts/test/test_files/imports/package.nt | 2 +- scripts/test/test_files/views/package-expanded.nt | 2 +- scripts/test/test_files/views/package.nt | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/scripts/test/test_files/NCBI_GenBank_imports.gb b/scripts/test/test_files/NCBI_GenBank_imports.gb index e0627fac..6c8cfc32 100644 --- a/scripts/test/test_files/NCBI_GenBank_imports.gb +++ b/scripts/test/test_files/NCBI_GenBank_imports.gb @@ -8,7 +8,7 @@ DBLINK BioProject: PRJNA266657 KEYWORDS WGS. SOURCE Escherichia coli ORGANISM Escherichia coli - Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; + Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 3242) AUTHORS Tyson,G.H., McDermott,P.F., Li,C., Chen,Y., Tadesse,D.A., diff --git a/scripts/test/test_files/distribution/distribution.nt b/scripts/test/test_files/distribution/distribution.nt index 4ea52d3f..99530473 100644 --- a/scripts/test/test_files/distribution/distribution.nt +++ b/scripts/test/test_files/distribution/distribution.nt @@ -2183,7 +2183,7 @@ "WGS." . "JWYZ01000115" . "DNA" . - "Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . + "Escherichia coli Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . . . "Escherichia coli" . diff --git a/scripts/test/test_files/imports/imports_test_ncbi.gb b/scripts/test/test_files/imports/imports_test_ncbi.gb index e0627fac..6c8cfc32 100644 --- a/scripts/test/test_files/imports/imports_test_ncbi.gb +++ b/scripts/test/test_files/imports/imports_test_ncbi.gb @@ -8,7 +8,7 @@ DBLINK BioProject: PRJNA266657 KEYWORDS WGS. SOURCE Escherichia coli ORGANISM Escherichia coli - Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; + Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia. REFERENCE 1 (bases 1 to 3242) AUTHORS Tyson,G.H., McDermott,P.F., Li,C., Chen,Y., Tadesse,D.A., diff --git a/scripts/test/test_files/imports/package.nt b/scripts/test/test_files/imports/package.nt index d6c44fc2..097a1f8d 100644 --- a/scripts/test/test_files/imports/package.nt +++ b/scripts/test/test_files/imports/package.nt @@ -914,7 +914,7 @@ "WGS." . "JWYZ01000115" . "DNA" . - "Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . + "Escherichia coli Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . . . "Escherichia coli" . diff --git a/scripts/test/test_files/views/package-expanded.nt b/scripts/test/test_files/views/package-expanded.nt index 5096ab01..9e74118e 100644 --- a/scripts/test/test_files/views/package-expanded.nt +++ b/scripts/test/test_files/views/package-expanded.nt @@ -2170,7 +2170,7 @@ "WGS." . "JWYZ01000115" . "DNA" . - "Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . + "Escherichia coli Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . . . "Escherichia coli" . diff --git a/scripts/test/test_files/views/package.nt b/scripts/test/test_files/views/package.nt index 343be30b..52dcd744 100644 --- a/scripts/test/test_files/views/package.nt +++ b/scripts/test/test_files/views/package.nt @@ -1799,7 +1799,7 @@ "WGS." . "JWYZ01000115" . "DNA" . - "Escherichia coli Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . + "Escherichia coli Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia." . . . "Escherichia coli" . From 1fdbf69e9d724199660a9ed4d246687a3b81b1ad Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Fri, 31 Mar 2023 20:23:51 +0000 Subject: [PATCH 2/2] Build distribution --- distribution.gb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/distribution.gb b/distribution.gb index b09ceaf2..60f4605c 100644 --- a/distribution.gb +++ b/distribution.gb @@ -14381,14 +14381,14 @@ FEATURES Location/Qualifiers /label="D1002" misc_feature 255..425 /label="D2002" - promoter 181..243 + misc_feature 181..243 /label="pBetI" misc_feature 1..425 ORIGIN 1 aacgatgatg ctcactctcg ggtaccagca ttttcggagg ttctctaaca gtatggataa 61 ccgtgttttc actgtgctgc ggttacccat cgcctgaaat ccagttggtg tcaagccatt 121 ccctgtctag gacgccgcat gtagtaaaac atatacattg ctcgggttcg gtctcgggag - 181 agcgcgggtg agagggattc gttaccaatt gacaattgat tggacgttca atataatgct + 181 agcgcgggtg agagggattc gttaccaata gacaattgat tggacgttca atataatgct 241 agctacttga gacctataaa cgccaggttg tatccgcatt tgatgctacc atggatgagt 301 cagcgtcgag cacgcggcat ttattgcatg agtagggttg actaagaacc gttagatgcc 361 tcgctgtact aataattgtc aacagatcgt caagattaga aaatagggtt tagtccggca