From 3392109f5b7507283029e2c3222261d775555743 Mon Sep 17 00:00:00 2001 From: Seth Carbon Date: Thu, 11 Jun 2020 16:44:27 -0700 Subject: [PATCH 1/2] add test rule for #1514 --- metadata/rules/gorule-0000001.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/metadata/rules/gorule-0000001.md b/metadata/rules/gorule-0000001.md index b37958ea..580c2f65 100644 --- a/metadata/rules/gorule-0000001.md +++ b/metadata/rules/gorule-0000001.md @@ -9,6 +9,12 @@ contact: "go-quality@mailman.stanford.edu" implementations: - language: python source: https://github.com/biolink/ontobio/blob/master/ontobio/io/gafparser.py +examples: + repair: + - comment: CJK can pass through without modification + format: gaf + input: "FB FBgn0033449 CG1663 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 FlyBase" + output: "FB FBgn0033449 CG1663 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 FlyBase" --- Each line of a GAF file is checked that it generally conforms to the GAF 2.1 spec and some GO specific specifications. The GAF 2.1 spec is here: http://geneontology.org/page/go-annotation-file-gaf-format-21. @@ -16,4 +22,4 @@ GO specific specifications. The GAF 2.1 spec is here: http://geneontology.org/pa Qualifier, evidence, aspect and DB object columns must be within the list of allowed values (as per the spec). -Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details). \ No newline at end of file +Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details). From 786827eeb815dce218ff9a40c7d7d6c839bcf6d5 Mon Sep 17 00:00:00 2001 From: Seth Carbon Date: Thu, 11 Jun 2020 17:20:27 -0700 Subject: [PATCH 2/2] examples for #1514 --- metadata/rules/gorule-0000001.md | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/metadata/rules/gorule-0000001.md b/metadata/rules/gorule-0000001.md index 580c2f65..9e0e3d15 100644 --- a/metadata/rules/gorule-0000001.md +++ b/metadata/rules/gorule-0000001.md @@ -11,10 +11,18 @@ implementations: source: https://github.com/biolink/ontobio/blob/master/ontobio/io/gafparser.py examples: repair: - - comment: CJK can pass through without modification + - comment: (UTF-8) CJK can pass through without modification (隣のトトロ) format: gaf - input: "FB FBgn0033449 CG1663 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 FlyBase" - output: "FB FBgn0033449 CG1663 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 FlyBase" + input: "FB FBgn0033449 隣のトトロ GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 FlyBase" + output: "FB FBgn0033449 隣のトトロ GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 FlyBase" + - comment: (UTF-8) Accent marks can pass through without modification (Astérix_le_Gaulois) + format: gaf + input: "FB FBgn0033449 123_456 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 Astérix_le_Gaulois" + output: "FB FBgn0033449 123_456 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 Astérix_le_Gaulois" + - comment: (UTF-8) Greek latters can pass through without modification (αΩ) + format: gaf + input: "α FBgn0033449 123_456 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 Ω" + output: "α FBgn0033449 123_456 GO:1902361 FB:FBrf0202953|GO_REF:0000024 ISS UniProtKB:Q05516 F protein taxon:7227 20171127 Ω" --- Each line of a GAF file is checked that it generally conforms to the GAF 2.1 spec and some GO specific specifications. The GAF 2.1 spec is here: http://geneontology.org/page/go-annotation-file-gaf-format-21.