examples

solislemuslab · Jan 17, 2024 · 342d487 · 342d487
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diff --git a/example/README.md → examples/README.md b/example/README.md → examples/README.md
@@ -1,6 +1,6 @@
 # Examples
 
-The purpose of this folder is to provide worked example of MiNAA's inputs, execution, and outputs.
+The purpose of this directory is to provide worked example of MiNAA's inputs, execution, and outputs.
 
 `g.csv` is the adjacency matrix for the network G.
 `h.csv` is the adjacency matrix for the network H.
@@ -10,23 +10,23 @@ Once MiNAA is successfully compiled, the examples below can be run from this pro
 
 ## Example 1
 
-`./minaa.exe example/g.csv example/h.csv -a=0.6 -g`
+`./minaa.exe examples/g.csv examples/h.csv -a=0.6 -g`
 
 Output to: `g-h-a0.6/`
 
 Here we align network **g** with network **h** using no biological data. `-a=0.6` sets alpha equal to 0.6, meaning 60% of the topological cost function comes from similarity calculated by GDVs, and 40% from simpler node degree data.
 
 ## Example 2
 
-`./minaa.exe example/g.csv example/h.csv -B=example/bio.csv -b=0.85 -st=0.5 -s`
+`./minaa.exe examples/g.csv examples/h.csv -B=examples/bio.csv -b=0.85 -st=0.5 -s`
 
 Output to: `g-h/`
 
 Here we align network **g** with network **h** using topological information and the given biological similarity matrix, **bio**. Since we've provided a similarity matrix instead of a cost matrix (the default), we have to flag that with `-s`. Since alpha was unspecified, it defaults to 1. Since beta was set to 0.85, 85% of the cost weight is from the calculated topological cost matrix, and 15% is from **bio**. Since the similarity threshold `-st=` was set to 0.5, any aligned pair with similarity score less than or equal to 0.5 is excluded from the alignment results.
 
 ## Example 3
 
-`./minaa.exe example/g.csv example/h.csv -Galias=nonsmoker -Halias=smoker -p -t`
+`./minaa.exe examples/g.csv examples/h.csv -Galias=nonsmoker -Halias=smoker -p -t`
 
 Output to: `nonsmoker-smoker-2024_01_16-22_05_34/`
 

diff --git a/example/bio.csv → examples/bio.csv b/example/bio.csv → examples/bio.csv
diff --git a/example/g-h-a0.6/alignment_list.csv → examples/g-h-a0.6/alignment_list.csv b/example/g-h-a0.6/alignment_list.csv → examples/g-h-a0.6/alignment_list.csv
diff --git a/example/g-h-a0.6/alignment_matrix.csv → examples/g-h-a0.6/alignment_matrix.csv b/example/g-h-a0.6/alignment_matrix.csv → examples/g-h-a0.6/alignment_matrix.csv
diff --git a/example/g-h-a0.6/g_gdvs.csv → examples/g-h-a0.6/g_gdvs.csv b/example/g-h-a0.6/g_gdvs.csv → examples/g-h-a0.6/g_gdvs.csv
diff --git a/example/g-h-a0.6/h_gdvs.csv → examples/g-h-a0.6/h_gdvs.csv b/example/g-h-a0.6/h_gdvs.csv → examples/g-h-a0.6/h_gdvs.csv
diff --git a/example/g-h-a0.6/log.txt → examples/g-h-a0.6/log.txt b/example/g-h-a0.6/log.txt → examples/g-h-a0.6/log.txt
@@ -1,12 +1,12 @@
-Executing:   ./minaa.exe example/g.csv example/h.csv -a=0.6 -g 
+Executing:   ./minaa.exe examples/g.csv examples/h.csv -a=0.6 -g 
 Y_M_D-H_M_S: 2024_01_16-22_02_40
 
 INPUTS
 G File:               g.csv
 H File:               h.csv
 Alpha:                0.600
 Beta:                 1.000
-Similarity threshold: 0.0000
+Similarity threshold: 0.000
 
 BEGINNING ALIGNMENT
 Reading graph files............................done. (9ms)

diff --git a/example/g-h-a0.6/topological_costs.csv → examples/g-h-a0.6/topological_costs.csv b/example/g-h-a0.6/topological_costs.csv → examples/g-h-a0.6/topological_costs.csv
diff --git a/example/g-h/alignment_list.csv → examples/g-h/alignment_list.csv b/example/g-h/alignment_list.csv → examples/g-h/alignment_list.csv
diff --git a/example/g-h/alignment_matrix.csv → examples/g-h/alignment_matrix.csv b/example/g-h/alignment_matrix.csv → examples/g-h/alignment_matrix.csv
diff --git a/example/g-h/g_gdvs.csv → examples/g-h/g_gdvs.csv b/example/g-h/g_gdvs.csv → examples/g-h/g_gdvs.csv
diff --git a/example/g-h/h_gdvs.csv → examples/g-h/h_gdvs.csv b/example/g-h/h_gdvs.csv → examples/g-h/h_gdvs.csv
diff --git a/example/g-h/log.txt → examples/g-h/log.txt b/example/g-h/log.txt → examples/g-h/log.txt
@@ -1,4 +1,4 @@
-Executing:   ./minaa.exe example/g.csv example/h.csv -B=example/bio.csv -b=0.85 -st=0.5 -s 
+Executing:   ./minaa.exe examples/g.csv examples/h.csv -B=examples/bio.csv -b=0.85 -st=0.5 -s 
 Y_M_D-H_M_S: 2024_01_16-22_00_30
 
 INPUTS

diff --git a/example/g-h/overall_costs.csv → examples/g-h/overall_costs.csv b/example/g-h/overall_costs.csv → examples/g-h/overall_costs.csv
diff --git a/example/g-h/topological_costs.csv → examples/g-h/topological_costs.csv b/example/g-h/topological_costs.csv → examples/g-h/topological_costs.csv
diff --git a/example/g.csv → examples/g.csv b/example/g.csv → examples/g.csv
diff --git a/example/h.csv → examples/h.csv b/example/h.csv → examples/h.csv
diff --git a/...er-2024_01_16-23_10_14/alignment_list.csv → ...er-2024_01_16-23_10_14/alignment_list.csv b/...er-2024_01_16-23_10_14/alignment_list.csv → ...er-2024_01_16-23_10_14/alignment_list.csv
diff --git a/...-2024_01_16-23_10_14/alignment_matrix.csv → ...-2024_01_16-23_10_14/alignment_matrix.csv b/...-2024_01_16-23_10_14/alignment_matrix.csv → ...-2024_01_16-23_10_14/alignment_matrix.csv
diff --git a/...smoker-smoker-2024_01_16-23_10_14/log.txt → ...smoker-smoker-2024_01_16-23_10_14/log.txt b/...smoker-smoker-2024_01_16-23_10_14/log.txt → ...smoker-smoker-2024_01_16-23_10_14/log.txt
@@ -1,4 +1,4 @@
-Executing:   ./minaa.exe example/g.csv example/h.csv -Galias=nonsmoker -Halias=smoker -p -t 
+Executing:   ./minaa.exe examples/g.csv examples/h.csv -Galias=nonsmoker -Halias=smoker -p -t 
 Y_M_D-H_M_S: 2024_01_16-23_10_14
 
 INPUTS

diff --git a/...-smoker-2024_01_16-23_10_14/nonsmoker.csv → ...-smoker-2024_01_16-23_10_14/nonsmoker.csv b/...-smoker-2024_01_16-23_10_14/nonsmoker.csv → ...-smoker-2024_01_16-23_10_14/nonsmoker.csv
diff --git a/...er-2024_01_16-23_10_14/nonsmoker_gdvs.csv → ...er-2024_01_16-23_10_14/nonsmoker_gdvs.csv b/...er-2024_01_16-23_10_14/nonsmoker_gdvs.csv → ...er-2024_01_16-23_10_14/nonsmoker_gdvs.csv
diff --git a/...ker-smoker-2024_01_16-23_10_14/smoker.csv → ...ker-smoker-2024_01_16-23_10_14/smoker.csv b/...ker-smoker-2024_01_16-23_10_14/smoker.csv → ...ker-smoker-2024_01_16-23_10_14/smoker.csv
diff --git a/...moker-2024_01_16-23_10_14/smoker_gdvs.csv → ...moker-2024_01_16-23_10_14/smoker_gdvs.csv b/...moker-2024_01_16-23_10_14/smoker_gdvs.csv → ...moker-2024_01_16-23_10_14/smoker_gdvs.csv
diff --git a/...2024_01_16-23_10_14/topological_costs.csv → ...2024_01_16-23_10_14/topological_costs.csv b/...2024_01_16-23_10_14/topological_costs.csv → ...2024_01_16-23_10_14/topological_costs.csv