updating files to use node_A instead of A

Reed-CompBio · Nov 4, 2024 · bec0b88 · bec0b88
1 parent 28321e0
commit bec0b88
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Showing 26 changed files with 39 additions and 39 deletions.
diff --git a/input/alternative-network.txt b/input/alternative-network.txt
@@ -1,6 +1,6 @@
-A	B	0.98	U
+node_A	B	0.98	U
 B	C	0.77	U
-A	D	0.12	U
+node_A	D	0.12	U
 C	D	0.89	U
 C	E	0.59	U
 C	F	0.50	U

diff --git a/input/gs_nodes0.txt b/input/gs_nodes0.txt
@@ -1,2 +1,2 @@
-A
+node_A
 B
diff --git a/input/network.txt b/input/network.txt
@@ -1,2 +1,2 @@
-A	B	0.98	U
+node_A	B	0.98	U
 B	C	0.77	U
diff --git a/input/node-prizes.txt b/input/node-prizes.txt
@@ -1,3 +1,3 @@
 NODEID	prize	active
-A	2	true
+node_A	2	true
 C	5.7	true
diff --git a/input/sources.txt b/input/sources.txt
@@ -1 +1 @@
-A
+node_A
diff --git a/test/generate-inputs/expected/allpairs-network-expected.txt b/test/generate-inputs/expected/allpairs-network-expected.txt
@@ -1,3 +1,3 @@
 #Interactor1	Interactor2	Weight
-A	B	0.98
+node_A	B	0.98
 B	C	0.77
diff --git a/test/generate-inputs/expected/domino-network-expected.txt b/test/generate-inputs/expected/domino-network-expected.txt
@@ -1,3 +1,3 @@
 ID_interactor_A	ppi	ID_interactor_B
-ENSG0A	ppi	ENSG0B
+ENSG0node_A	ppi	ENSG0B
 ENSG0B	ppi	ENSG0C
diff --git a/test/generate-inputs/expected/meo-edges-expected.txt b/test/generate-inputs/expected/meo-edges-expected.txt
@@ -1,2 +1,2 @@
-A	(pp)	B	0.98
+node꧁SEP꧂A	(pp)	B	0.98
 B	(pp)	C	0.77
diff --git a/test/generate-inputs/expected/mincostflow-edges-expected.txt b/test/generate-inputs/expected/mincostflow-edges-expected.txt
@@ -1,4 +1,4 @@
-A	B	0.98
+node_A	B	0.98
 B	C	0.77
-B	A	0.98
+B	node_A	0.98
 C	B	0.77
diff --git a/test/generate-inputs/expected/omicsintegrator1-edges-expected.txt b/test/generate-inputs/expected/omicsintegrator1-edges-expected.txt
@@ -1,3 +1,3 @@
 protein1	protein2	weight	directionality
-A	B	0.98	U
+node_A	B	0.98	U
 B	C	0.77	U
diff --git a/test/generate-inputs/expected/omicsintegrator2-edges-expected.txt b/test/generate-inputs/expected/omicsintegrator2-edges-expected.txt
@@ -1,3 +1,3 @@
 protein1	protein2	cost
-A	B	0.52
+node_A	B	0.52
 B	C	0.73
diff --git a/test/generate-inputs/expected/pathlinker-network-expected.txt b/test/generate-inputs/expected/pathlinker-network-expected.txt
@@ -1,5 +1,5 @@
 #Interactor1	Interactor2	Weight
-A	B	0.98
+node_A	B	0.98
 B	C	0.77
-B	A	0.98
+B	node_A	0.98
 C	B	0.77
diff --git a/test/parse-outputs/expected/allpairs-pathway-expected.txt b/test/parse-outputs/expected/allpairs-pathway-expected.txt
@@ -1,8 +1,8 @@
 Node1	Node2	Rank	Direction
-S1	A	1	U
+S1	node_A	1	U
 S1	B	1	U
-A	E	1	U
-A	F	1	U
+node_A	E	1	U
+node_A	F	1	U
 E	T1	1	U
 T1	F	1	U
 F	T2	1	U

diff --git a/test/parse-outputs/expected/meo-pathway-expected.txt b/test/parse-outputs/expected/meo-pathway-expected.txt
@@ -1,3 +1,3 @@
 Node1	Node2	Rank	Direction
-GENE_A	GENE_C	1	D
-GENE_C	GENEB	1	D
+node_A	C	1	D
+C	B	1	D
diff --git a/test/parse-outputs/expected/mincostflow-pathway-expected.txt b/test/parse-outputs/expected/mincostflow-pathway-expected.txt
@@ -1,3 +1,3 @@
 Node1	Node2	Rank	Direction
-B	A	1	U
+B	node_A	1	U
 D	B	1	U
diff --git a/test/parse-outputs/expected/omicsintegrator1-pathway-expected.txt b/test/parse-outputs/expected/omicsintegrator1-pathway-expected.txt
@@ -1,3 +1,3 @@
 Node1	Node2	Rank	Direction
-A	C	1	D
+node_A	C	1	D
 C	D	1	U
diff --git a/test/parse-outputs/expected/omicsintegrator2-pathway-expected.txt b/test/parse-outputs/expected/omicsintegrator2-pathway-expected.txt
@@ -1,3 +1,3 @@
 Node1	Node2	Rank	Direction
-B	A	1	U
+B	node_A	1	U
 B	C	1	U
diff --git a/test/parse-outputs/expected/pathlinker-pathway-expected.txt b/test/parse-outputs/expected/pathlinker-pathway-expected.txt
@@ -1,7 +1,7 @@
 Node1	Node2	Rank	Direction
 S2	T3	1	D
-A	E	2	D
-S1	A	2	D
+node_A	E	2	D
+S1	node_A	2	D
 E	T1	2	D
 B	F	3	D
 F	T2	3	D
@@ -15,4 +15,4 @@ E	F	7	D
 B	C	8	D
 F	E	11	D
 G	F	13	D
-F	A	16	D
+F	node_A	16	D
diff --git a/test/parse-outputs/input/allpairs-raw-pathway.txt b/test/parse-outputs/input/allpairs-raw-pathway.txt
@@ -1,7 +1,7 @@
-S1	A
+S1	node_A
 S1	B
-A	E
-A	F
+node_A	E
+node_A	F
 E	T1
 T1	F
 F	T2

diff --git a/test/parse-outputs/input/meo-raw-pathway.txt b/test/parse-outputs/input/meo-raw-pathway.txt
@@ -1,3 +1,3 @@
 Source	Type	Target	Oriented	Weight
-GENE꧁SEP꧂A	pp	GENE꧁SEP꧂C	true	0.5
-GENE꧁SEP꧂C	pd	GENEB	true	0.5
+node꧁SEP꧂A	pp	C	true	0.5
+C	pd	B	true	0.5
diff --git a/test/parse-outputs/input/mincostflow-raw-pathway.txt b/test/parse-outputs/input/mincostflow-raw-pathway.txt
@@ -1,2 +1,2 @@
-B	A
+B	node_A
 D	B
diff --git a/...outputs/input/omicsintegrator-edge-cases/omicsintegrator2-miss-insolution-raw-pathway.txt b/...outputs/input/omicsintegrator-edge-cases/omicsintegrator2-miss-insolution-raw-pathway.txt
@@ -1,3 +1,3 @@
 protein1	protein2	cost
-B	A	0.52
+B	node_A	0.52
 B	C	0.73
diff --git a/...rse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-wrong-order-raw-pathway.txt b/...rse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-wrong-order-raw-pathway.txt
@@ -1,3 +1,3 @@
 protein1	protein2	in_solution	cost
-B	A	True	0.52
+B	node_A	True	0.52
 B	C	True	0.73
diff --git a/test/parse-outputs/input/omicsintegrator1-raw-pathway.txt b/test/parse-outputs/input/omicsintegrator1-raw-pathway.txt
@@ -1,2 +1,2 @@
-A	pd	C
+node_A	pd	C
 C	pp	D
diff --git a/test/parse-outputs/input/omicsintegrator2-raw-pathway.txt b/test/parse-outputs/input/omicsintegrator2-raw-pathway.txt
@@ -1,3 +1,3 @@
 protein1	protein2	cost	in_solution
-B	A	0.52	True
+B	node_A	0.52	True
 B	C	0.73	True
diff --git a/test/parse-outputs/input/pathlinker-raw-pathway.txt b/test/parse-outputs/input/pathlinker-raw-pathway.txt
@@ -1,7 +1,7 @@
 #tail	head	KSP index	path cost
 S2	T3	1	5.00000e-01
-A	E	2	1.25000e-01
-S1	A	2	1.25000e-01
+node_A	E	2	1.25000e-01
+S1	node_A	2	1.25000e-01
 E	T1	2	1.25000e-01
 B	F	3	1.25000e-01
 F	T2	3	1.25000e-01
@@ -15,4 +15,4 @@ E	F	7	6.25000e-02
 B	C	8	6.25000e-02
 F	E	11	6.25000e-02
 G	F	13	6.25000e-02
-F	A	16	3.12500e-02
+F	node_A	16	3.12500e-02
-Original file line number
+Diff line change
@@ -1,2 +1,2 @@
-    A
+    node_A
     B