Cleaned up repo

Author: melkebir

result/sims/machina/collect_clusterings.sh

@@ -0,0 +1,43 @@
+#!/bin/bash
+if [ ! $# -eq 3 ]
+then
+    echo "Usage: $0 <cluster_executable> <generatemutationtrees_executable> <pmh_ti_executable>" >&2
+    exit 1
+fi
+
+
+
+for m in {m5,m8}
+do
+    if [ ! -e input_${m} ]
+    then
+	mkdir input_${m}
+    fi
+
+    if [ ! -e mut_trees_${m} ]
+    then
+	mkdir mut_trees_${m}
+    fi
+
+    if [ ! -e output_${m} ]
+    then
+	mkdir output_${m}
+    fi
+
+    for p in {mS,S,M,R}
+    do
+        for f in ../../../data/sims/${m}/$p/reads_seed*.tsv
+        do
+    	    s=$(basename $f .tsv | sed -e s/reads_seed//g)
+
+	    echo Solving seed $s, pattern $p, anatomical sites $m...
+	    $1 -a 0.001 -b 0.05 $f > input_${m}/cluster_${p}_seed${s}.tsv 2> input_${m}/cluster_${p}_seed${s}.txt
+	    $2 input_${m}/cluster_${p}_seed${s}.tsv > mut_trees_${m}/mut_trees_${p}_seed${s}.txt
+	    if [ ! -e output_${m}/${p}_${s} ]
+	    then
+		mkdir output_${m}/${p}_${s}
+	    fi
+            $3 -p P -c ../../../data/sims/coloring.txt -m 1,2,3 -t 2 -o output_${m}/${p}_${s}/ -F input_${m}/cluster_${p}_seed${s}.tsv -barT mut_trees_${m}/mut_trees_${p}_seed${s}.txt > output_${m}/${p}_${s}.txt
+        done
+    done
+done