--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spatial_proximity.py	Sat Mar 31 14:09:14 2012 -0400
@@ -0,0 +1,36 @@
+
+import os,sys
+
+file1 = sys.argv[1]
+file2 = sys.argv[2]
+genome = sys.argv[3]
+outplot = sys.argv[4]
+outlog = sys.argv[5]
+outbed = sys.argv[6]
+
+strandness = ''
+if len(sys.argv) > 7:   
+    strandness = sys.argv[7]
+
+# real distance
+cmd = 'closestBed -a '+file1+' -b '+file2 + ' '+strandness + ' -d -t first > '+outbed
+os.system(cmd)
+# shuffle
+cmd = 'shuffleBed -chrom -g '+genome+' -i '+file1+'> shuffled.bed'
+os.system(cmd)
+# shuffled distance
+cmd = 'closestBed -a shuffled.bed -b '+file2 + ' '+strandness + ' -d -t first > shuffled.dist'
+os.system(cmd)
+
+
+# test in R
+r = open('tmp.r','w')
+r.write("options(warn=-1)\n")
+r.write("source('/Users/xuebing/galaxy-dist/tools/mytools/cdf.r')\n")
+r.write("x = read.table('"+outbed+"',sep='\t')\n")
+r.write("y = read.table('shuffled.dist',sep='\t')\n")
+r.write("pdf('"+outplot+"')\n")
+r.write("mycdf(list(log10(1+x[,ncol(x)]),log10(1+y[,ncol(y)])),'spatial distance',c('real','shuffled'),'topleft','log10 distance','')\n")
+r.write("dev.off()\n")
+r.close()
+os.system("R --vanilla < tmp.r >"+outlog)