Add test files for goatools

README.md

@@ -1076,13 +1076,19 @@ The earth sciences folder contain subfolders for different data formats encounte
     - 'ipython_notebook.md': exemplary markdown notebook
   - rmarkdown
     - 'rmarkdown_notebook.Rmd': exemplary R notebook
+- gene_ontology
+  - 'ontology.obo': a mock gene ontology with 5 terms.
+  - 'ontology_slim.obo': a mock GO slim with 2 terms.
+  - 'go_annotation.gaf': a mock GO annotation in GAF format, containing annotations for 8 genes.	
 - tsv
   - 'test.tsv': exemplary tab-separated file obtained from [here](https://bioinf.shenwei.me/csvtk/usage/#split)
   - 'ani.tsv': exemplary tab-seperated file describing pairwise similarities from [here](https://github.com/refresh-bio/clusty).
 - txt
   - 'hello.txt': one-line txt file
   - 'taxonomy_ids.txt': contains species names, to be used as input for [goat-cli taxon search tool](https://github.com/genomehubs/goat-cli).
   - 'ani_ids.txt': list of ids associated with 'tsv/ani.tsv' used as an input for [clusty](https://github.com/refresh-bio/clusty).
+  - 'sample_genes.txt': a list of 3 sample genes for GO enrichment analysis.
+  - 'population_genes.txt': a list of 9 population genes for GO enrichment analysis.
 - tar
   - 'hello.tar.gz': gzipped tar archive containing a single file without a directory
 

data/generic/gene_ontology/go_annotation.gaf

@@ -0,0 +1,13 @@
+!gaf-version: 2.1
+!
+!Mock GAF for testing enrichment tool
+!Generated: 2023-10-27
+!
+MockDB  A       GENE_A          GO:0000004      PMID:123        IMP             P       Metabolism Gene A               gene    taxon:9606      20231027        MockSource		
+MockDB  B       GENE_B          GO:0000004      PMID:123        IMP             P       Metabolism Gene B               gene    taxon:9606      20231027        MockSource		
+MockDB  C       GENE_C          GO:0000002      PMID:456        IDA             P       Metabolism Gene C               gene    taxon:9606      20231027        MockSource		
+MockDB  D       GENE_D          GO:0000001      PMID:789        TAS             P       General Gene D          gene    taxon:9606      20231027        MockSource		
+MockDB  E       GENE_E          GO:0000001      PMID:789        TAS             P       General Gene E          gene    taxon:9606      20231027        MockSource		
+MockDB  X       GENE_X          GO:0000005      PMID:101        IMP             P       Defense Gene X          gene    taxon:9606      20231027        MockSource		
+MockDB  Y       GENE_Y          GO:0000005      PMID:101        IMP             P       Defense Gene Y          gene    taxon:9606      20231027        MockSource		  
+MockDB  Z       GENE_Z          GO:0000003      PMID:202        IDA             P       Defense Gene Z          gene    taxon:9606      20231027        MockSource		

data/generic/gene_ontology/ontology.obo

@@ -0,0 +1,31 @@
+format-version: 1.2
+default-namespace: mock_ontology
+
+[Term]
+id: GO:0000001
+name: cellular_process
+def: "A broad biological process."
+
+[Term]
+id: GO:0000002
+name: metabolic_process
+def: "Chemical reactions within a cell."
+is_a: GO:0000001 ! cellular_process
+
+[Term]
+id: GO:0000003
+name: defense_response
+def: "Response to external stimuli."
+is_a: GO:0000001 ! cellular_process
+
+[Term]
+id: GO:0000004
+name: carbohydrate_metabolism
+def: "Breaking down sugars."
+is_a: GO:0000002 ! metabolic_process
+
+[Term]
+id: GO:0000005
+name: viral_defense
+def: "Specific defense against viruses."
+is_a: GO:0000003 ! defense_response

data/generic/gene_ontology/ontology_slim.obo

@@ -0,0 +1,12 @@
+format-version: 1.2
+ontology: mock_slim
+
+[Term]
+id: GO:0000002
+name: metabolic_process
+namespace: biological_process
+
+[Term]
+id: GO:0000003
+name: defense_response
+namespace: biological_process

data/generic/txt/population_genes.txt

@@ -0,0 +1,9 @@
+A
+B
+C
+D
+E
+F
+X
+Y
+Z

data/generic/txt/sample_genes.txt

@@ -0,0 +1,3 @@
+A
+B
+C