--- a/spatial_proximity.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-
-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)