modified: cre.sv.validate_bed.py

	new file:   cre.tstv.check.sh

cre.sv.validate_bed.py

@@ -16,7 +16,7 @@
 
 
 EVENT_SIZES = [(50, 100), (100, 300), (300, 500), (500, 1000), (1000, 10000),
-               (10000, int(1e6))]
+               (10000, 100000), (100000,int(1e6))]
 
 def _test(caller, svtype, size_range, ensemble, truth, data):
     efeats = pybedtools.BedTool(ensemble).sort().merge().saveas()
@@ -37,7 +37,7 @@ def _test(caller, svtype, size_range, ensemble, truth, data):
         for size in EVENT_SIZES:
             str_size = "%s-%s" % size
 #            _test(vcaller,svtype,size,sys.argv[1],sys.argv[2],data)
-            evalout = validate_evaluate_one(vcaller,svtype,size,sys.argv[1],sys.argv[2],data)
+            evalout = validate._evaluate_one(vcaller,svtype,size,sys.argv[1],sys.argv[2],data)
             writer.writerow([svtype, str_size, vcaller,
                              evalout["sensitivity"]["label"], evalout["precision"]["label"]])
             for metric in ["sensitivity", "precision"]:

cre.tstv.check.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+for f in *x/*;
+do 
+    if [ -f  ${f}/multiqc/multiqc_data/multiqc_data_final.json ]; 
+    then 
+	for g in `cat $f/multiqc/multiqc_data/multiqc_data_final.json | grep generalstats-tstv | awk -F ':' '{print $2}' | grep -v mqc | sed s/" "// | sed s/","//`;
+	do 
+	    echo $f $g >> tstv_check.txt;
+	done;
+    else
+	for g in `cat $f/multiqc/multiqc_data/multiqc_bcftools_stats.txt | sed 1d | awk '{print $6}'`;
+	do
+	    echo $f $g  >> tstv_check.txt;
+	done;
+    fi
+done;
+
+cat tstv_check.txt | sort -n -k2,2 > tstv_check_sorted.txt