psf to bedpe converter

phase/psf-to-bedpe.awk

@@ -0,0 +1,31 @@
+## USAGE: awk -f psf-to-bedpe.awk <path_to_psf_file> 
+## INPUT: psf file
+## OUTPUT: stdout in bedpe format
+## Written by O.D. (olga.dudchenko@bcm.edu)
+## Version: 02/09/22
+
+# print header
+BEGIN{
+    OFS="\t"
+    lenPerSnp=1000
+    end=0
+    print "#chr1", "x1", "x2", "chr2", "y1", "y2", "name", "score", "strand1", "strand2", "color"
+}
+# read psf properties part
+$0~/^>/{
+	chr[$5]=substr($1,2)
+	pos[$5]=$2
+	var1[$5]=$3
+	var2[$5]=$4
+	next
+}
+!scale{
+    scale=$(( 1 + 2*(NR-1)*lenPerSnp / 2100000000 ))
+}
+# read psf set part
+{
+    start=end; end+=int (NF*lenPerSnp/scale)
+    print "assembly", start, end, "assembly", start, end, chr[$1]":"pos[$1]":"var1[$1], ".", ".", ".", "0,0,255" 
+    start=end; end+=int (NF*lenPerSnp/scale)
+    print "assembly", start, end, "assembly", start, end, chr[$1]":"pos[$1]":"var2[$1], ".", ".", ".", "0,0,255" 
+}