Publication dateMar 9, 2022
Confidentiality public Public
GAF → GMT (GO_ALL + BP/MF/CC; withIEA/noIEA × id/symbol)
TASK
Typing name : TASK.gws_omix.GafToGmt Brick : gws_omix Builds GMT files from a GO GAF: GO_ALL (4 files) + split BP/MF/CC.
Convert GO annotations in GAF format into GMT gene set files.
Outputs:
- gmt_files (existing): GO_ALL × withIEA/noIEA × id/symbol (4 GMT)
- gmt_withIEA_by_go: BP/MF/CC × id/symbol (6 GMT, with IEA)
- gmt_noIEA_by_go: BP/MF/CC × id/symbol (6 GMT, excluding IEA)
Notes:
- 'NOT' annotations are always excluded.
- No term-size filtering is applied here (keep GMT complete).
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Input
GO Annotations (GAF/GAF.GZ)
Example: sgd.gaf.gz (yeast), fb.gaf.gz (drosophila).
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Output
GMT (GO_ALL)
A set of resources
GMT (withIEA) split by GO aspect
A set of resources
GMT (noIEA) split by GO aspect
A set of resources
settings
Configuration
Prefix for output GMT filenames.
Type : stringDefault value : organismTechnical bricks to reuse or customize Have you developed a brick?
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