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Add basic GAF pass-through check for UTF-8 #1515

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Add basic GAF pass-through check for UTF-8 #1515

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3392109
add test rule for #1514
kltm Jun 11, 2020
786827e
examples for #1514
kltm Jun 12, 2020
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16 changes: 15 additions & 1 deletion metadata/rules/gorule-0000001.md
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Expand Up @@ -9,11 +9,25 @@ contact: "[email protected]"
implementations:
- language: python
source: https://github.com/biolink/ontobio/blob/master/ontobio/io/gafparser.py
examples:
repair:
- comment: (UTF-8) CJK can pass through without modification (隣のトトロ)
format: gaf
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.

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).
Error report (number of errors) in [db_species]-summary.txt & owltools-check.txt (details).