From bec0b887beebd2c8e9a960bcca55da1ad6029bf9 Mon Sep 17 00:00:00 2001 From: ntalluri Date: Mon, 4 Nov 2024 12:29:32 -0600 Subject: [PATCH] updating files to use node_A instead of A --- input/alternative-network.txt | 4 ++-- input/gs_nodes0.txt | 2 +- input/network.txt | 2 +- input/node-prizes.txt | 2 +- input/sources.txt | 2 +- test/generate-inputs/expected/allpairs-network-expected.txt | 2 +- test/generate-inputs/expected/domino-network-expected.txt | 2 +- test/generate-inputs/expected/meo-edges-expected.txt | 2 +- .../generate-inputs/expected/mincostflow-edges-expected.txt | 4 ++-- .../expected/omicsintegrator1-edges-expected.txt | 2 +- .../expected/omicsintegrator2-edges-expected.txt | 2 +- .../expected/pathlinker-network-expected.txt | 4 ++-- test/parse-outputs/expected/allpairs-pathway-expected.txt | 6 +++--- test/parse-outputs/expected/meo-pathway-expected.txt | 4 ++-- .../parse-outputs/expected/mincostflow-pathway-expected.txt | 2 +- .../expected/omicsintegrator1-pathway-expected.txt | 2 +- .../expected/omicsintegrator2-pathway-expected.txt | 2 +- test/parse-outputs/expected/pathlinker-pathway-expected.txt | 6 +++--- test/parse-outputs/input/allpairs-raw-pathway.txt | 6 +++--- test/parse-outputs/input/meo-raw-pathway.txt | 4 ++-- test/parse-outputs/input/mincostflow-raw-pathway.txt | 2 +- .../omicsintegrator2-miss-insolution-raw-pathway.txt | 2 +- .../omicsintegrator2-wrong-order-raw-pathway.txt | 2 +- test/parse-outputs/input/omicsintegrator1-raw-pathway.txt | 2 +- test/parse-outputs/input/omicsintegrator2-raw-pathway.txt | 2 +- test/parse-outputs/input/pathlinker-raw-pathway.txt | 6 +++--- 26 files changed, 39 insertions(+), 39 deletions(-) diff --git a/input/alternative-network.txt b/input/alternative-network.txt index 439c556a..d81e5201 100644 --- 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 index 2fe4ab08..4401c534 100644 --- a/input/gs_nodes0.txt +++ b/input/gs_nodes0.txt @@ -1,2 +1,2 @@ -A +node_A B \ No newline at end of file diff --git a/input/network.txt b/input/network.txt index 9e8a9a68..359af809 100644 --- 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 index 0e1f682d..394551eb 100644 --- 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 index f70f10e4..4f668f5b 100644 --- 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 index 3cbac89c..8a1cd545 100644 --- 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 index 27683d36..f13ce400 100644 --- 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 index 5916b3d7..96d562b9 100644 --- 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 index f0889bf4..e16925c2 100644 --- 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 index 6342d481..37ba1f5f 100644 --- 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 index 997eb62e..bdfaf9c8 100644 --- 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 index d1f92741..13acd2f1 100644 --- 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 index 3af52bc6..d733dbd5 100644 --- 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 index 0023a8f7..529480df 100644 --- 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 index b25d172b..05249d3f 100644 --- 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 index f808bc3a..65d47433 100644 --- 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 index e34eeaff..85922a6e 100644 --- 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 index e490cd91..2833dd9f 100644 --- 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 index 8985411e..426c7064 100644 --- 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 index 9e1a6b8f..e8cda287 100644 --- 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 index 8c09120f..3a269f11 100644 --- 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/test/parse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-miss-insolution-raw-pathway.txt b/test/parse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-miss-insolution-raw-pathway.txt index 6ed53c89..294c9108 100644 --- a/test/parse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-miss-insolution-raw-pathway.txt +++ b/test/parse-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 \ No newline at end of file diff --git a/test/parse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-wrong-order-raw-pathway.txt b/test/parse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-wrong-order-raw-pathway.txt index bde8f08c..6ddca41f 100644 --- a/test/parse-outputs/input/omicsintegrator-edge-cases/omicsintegrator2-wrong-order-raw-pathway.txt +++ b/test/parse-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 \ No newline at end of file diff --git a/test/parse-outputs/input/omicsintegrator1-raw-pathway.txt b/test/parse-outputs/input/omicsintegrator1-raw-pathway.txt index ed72e753..a4805921 100644 --- 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 index ef24ed67..d812e130 100644 --- 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 index 25b13ae7..61112a82 100644 --- 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