Sync issue b15

RitchieLab · Jan 3, 2025 · 9c96b2f · 9c96b2f
1 parent 1d604f9
commit 9c96b2f
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Showing 12 changed files with 60 additions and 323 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/docs-dev/.DS_Store b/docs-dev/.DS_Store
diff --git a/docs-dev/Status_Reports_2_4_4/report_02/Technical_Report_02.docx b/docs-dev/Status_Reports_2_4_4/report_02/Technical_Report_02.docx
diff --git a/docs-dev/Status_Reports_2_4_4/report_02/Technical_Report_02.pdf b/docs-dev/Status_Reports_2_4_4/report_02/Technical_Report_02.pdf
diff --git a/tests/.DS_Store b/tests/.DS_Store
diff --git a/tests/issues/.DS_Store b/tests/issues/.DS_Store
diff --git a/tests/issues/b15_biofilter_group_annotation/data-in/TEST_SINGLE_GENE.txt b/tests/issues/b15_biofilter_group_annotation/data-in/TEST_SINGLE_GENE.txt
@@ -1 +1,2 @@
-ENSG00000000003
+ENSG00000055208
+ENSG00000228408
diff --git a/...tion/data-out/outcome_run_2.configuration → ...NAseq_ENSEMBL_gene_pathways.configuration b/...tion/data-out/outcome_run_2.configuration → ...NAseq_ENSEMBL_gene_pathways.configuration
@@ -1,5 +1,5 @@
 # Biofilter configuration file
-#   generated Tue, 03 Dec 2024 17:45:38
+#   generated Thu, 05 Dec 2024 15:25:55
 #   Biofilter version 2.4.4 (2024-12-01)
 #   LOKI version 2.2.5 (2019-03-15)
 
@@ -15,7 +15,7 @@ ALLOW_AMBIGUOUS_KNOWLEDGE           no
 REDUCE_AMBIGUOUS_KNOWLEDGE          no
 REPORT_LD_PROFILES                  no
 USER_DEFINED_FILTER                 no
-GENE_FILE                           /Users/andrerico/Works/Sys/biofilter/tests/issues/b15_biofilter_group_annotation/data-in/genes_out_from_run_1.txt
+GENE_FILE                           /Users/andrerico/Works/Sys/biofilter/tests/issues/b15_biofilter_group_annotation/data-in/TEST_SINGLE_GENE.txt
 GENE_IDENTIFIER_TYPE                ensembl_gid
 ALLOW_AMBIGUOUS_GENES               no
 GROUP_IDENTIFIER_TYPE               -
@@ -40,7 +40,7 @@ PARIS_BIN_SIZE                      10000
 PARIS_DETAILS                       no
 QUIET                               no
 VERBOSE                             yes
-PREFIX                              /Users/andrerico/Works/Sys/biofilter/tests/issues/b15_biofilter_group_annotation/data-out/outcome_run_2
+PREFIX                              /Users/andrerico/Works/Sys/biofilter/tests/issues/b15_biofilter_group_annotation/data-out/ROSMAP_RNAseq_ENSEMBL_gene_pathways
 OVERWRITE                           yes
 STDOUT                              no
 REPORT_INVALID_INPUT                no

diff --git a/...biofilter_group_annotation/data-out/ROSMAP_RNAseq_ENSEMBL_gene_pathways.gene-group-source b/...biofilter_group_annotation/data-out/ROSMAP_RNAseq_ENSEMBL_gene_pathways.gene-group-source
@@ -0,0 +1,50 @@
+#gene	group	source
+ENSG00000055208	protein binding	go
+ENSG00000055208	nucleoplasm	go
+ENSG00000055208	cytosol	go
+ENSG00000055208	plasma membrane	go
+ENSG00000055208	heart development	go
+ENSG00000055208	zinc ion binding	go
+ENSG00000055208	endosome membrane	go
+ENSG00000055208	negative regulation of autophagy	go
+ENSG00000055208	response to lipopolysaccharide	go
+ENSG00000055208	positive regulation of I-kappaB kinase/NF-kappaB signaling	go
+ENSG00000055208	positive regulation of protein kinase activity	go
+ENSG00000055208	K63-linked polyubiquitin modification-dependent protein binding	go
+ENSG00000055208	MAPK signaling pathway	kegg
+ENSG00000055208	NF-kappa B signaling pathway	kegg
+ENSG00000055208	Osteoclast differentiation	kegg
+ENSG00000055208	Toll-like receptor signaling pathway	kegg
+ENSG00000055208	NOD-like receptor signaling pathway	kegg
+ENSG00000055208	IL-17 signaling pathway	kegg
+ENSG00000055208	TNF signaling pathway	kegg
+ENSG00000055208	Alcoholic liver disease	kegg
+ENSG00000055208	Pathogenic Escherichia coli infection	kegg
+ENSG00000055208	Shigellosis	kegg
+ENSG00000055208	Salmonella infection	kegg
+ENSG00000055208	Yersinia infection	kegg
+ENSG00000055208	Leishmaniasis	kegg
+ENSG00000055208	Toxoplasmosis	kegg
+ENSG00000055208	Hepatitis B	kegg
+ENSG00000055208	Measles	kegg
+ENSG00000055208	Herpes simplex virus 1 infection	kegg
+ENSG00000055208	Epstein-Barr virus infection	kegg
+ENSG00000055208	Human immunodeficiency virus 1 infection	kegg
+ENSG00000055208	Coronavirus disease - COVID-19	kegg
+ENSG00000055208	Lipid and atherosclerosis	kegg
+ENSG00000055208	R-HSA-9645460	reactome
+ENSG00000055208	R-HSA-5607764	reactome
+ENSG00000055208	R-HSA-202424	reactome
+ENSG00000055208	R-HSA-2871837	reactome
+ENSG00000055208	R-HSA-937042	reactome
+ENSG00000055208	R-HSA-975163	reactome
+ENSG00000055208	R-HSA-9020702	reactome
+ENSG00000055208	R-HSA-450321	reactome
+ENSG00000055208	R-HSA-168638	reactome
+ENSG00000055208	R-HSA-1251985	reactome
+ENSG00000055208	R-HSA-9705671	reactome
+ENSG00000055208	R-HSA-445989	reactome
+ENSG00000055208	R-HSA-9014325	reactome
+ENSG00000055208	R-HSA-5357956	reactome
+ENSG00000055208	R-HSA-937072	reactome
+ENSG00000055208	R-HSA-450302	reactome
diff --git a/tests/issues/b15_biofilter_group_annotation/data-out/outcome_run_2.gene-group-source b/tests/issues/b15_biofilter_group_annotation/data-out/outcome_run_2.gene-group-source