# HG changeset patch
# User xuebing
# Date 1333234224 14400
# Node ID cce2eabe8b8d4ed0b1c0274be6f69e0b74954278
# Parent  b0e04c11263332d7fc96ed0877c0610ee278e911
Uploaded

diff -r b0e04c112633 -r cce2eabe8b8d bed_size_stat.py
--- a/bed_size_stat.py	Sat Mar 31 18:50:12 2012 -0400
+++ b/bed_size_stat.py	Sat Mar 31 18:50:24 2012 -0400
@@ -6,12 +6,17 @@
 
 inputfile = sys.argv[1]
 outputfile = sys.argv[2]
+log = sys.argv[3]
 
 rf = open('tmp.r','w')
 rf.write("x <- read.table('"+inputfile+"')\n")
 rf.write("len <- x[,3]-x[,2]\n")
 rf.write("pdf('"+outputfile+"')\n")
-rf.write("hist(len,breaks=100,xlab='interval size',main=paste('mean=',mean(len),sep=''))\n")
+if log == 'log':
+    rf.write("len <- log10(len+1)\n")
+    rf.write("hist(len,breaks=100,xlab='interval size',main=paste('mean=',mean(len),sep=''))\n")
+else:
+    rf.write("hist(len,breaks=100,xlab='interval size (log10)',main=paste('mean=',mean(len),sep=''))\n")
 rf.write("dev.off()")
 rf.close()
 os.system("R --vanilla < tmp.r")