--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwig_to_wig.sh	Tue Aug 05 07:44:03 2014 -0400
@@ -0,0 +1,77 @@
+#!/bin/bash
+#$Id: bigwig2wig 23 2014-01-28 12:09:22Z jens $
+
+#SCRIPT CONVERTS BIGWIG FILE TO FIXED-STEP WIGGLE FORMAT FILE
+#RESOLUTION IS CONTROLLED THROUGH THE BIN SIZE
+
+#default bin_size
+bin_size=500
+mylab="wiggle file"
+
+#parse input
+while getopts hf:b:l: myarg
+do	case "$myarg" in
+	h)	echo "Usage: bigwig_correlation -f <bigwig_file> -b <bin_size>"
+	        echo "Ex: bigwig_correlation -f <MYFILE.bw> -b 600"
+		exit ;;
+	f)	bigwig_file="$OPTARG" ;; #required
+	l)	mylab="$OPTARG" ;; #optional 
+	b)	bin_size="$OPTARG" ;; #optional
+	[?])	echo "Usage: bigwig_correlation -f <MYFILE.bw> -b <bin_size>"
+		exit 1 ;;
+	esac
+done
+
+###################################################
+###VALIDATE INPUT
+###################################################
+
+#make tmp-filename to hold chromosome info
+org_assembly_file=`mktemp -u`
+bigWigInfo -chroms $bigwig_file | perl -ne "/^\tchr/ && print" | perl -pe "s/ +/\t/g" | cut -f2,4 > $org_assembly_file
+
+#check bin_size & define step_size
+bin_size_mod=`expr $bin_size % 2`  #determine modulus
+if [ $bin_size_mod -ne 0 ]; then
+  echo "Chosen bin_size must be an even positive number, added +1 to bin_size"
+  bin_size=$(($bin_size + 1))
+fi
+
+if [ $bin_size -lt 100 ]; then
+  echo "ERROR: Chosen bin_size must be a positive number >=100"
+  exit 1
+fi
+#set stetp size equal to bin size i.e. non-overlapping intervals
+step_size=$bin_size
+
+###################################################
+###EXTRACT DENSITIES FROM NORMALIZED BIGWIG FILES
+###################################################
+
+
+#make track definition line
+echo "track type=wiggle_0 name=$mylab description=\"fixedStep format\"" 
+
+#for each chromsome
+cat $org_assembly_file | while read line; do
+ 
+  cur_chr=`echo $line | cut --delimiter=" " -f1`
+  cur_length=`echo $line | cut --delimiter=" " -f2`
+  
+  n_bins=`echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc`
+ 
+  start=1
+  stop=`echo "$n_bins * $bin_size" | bc`
+
+  #write header line for each chromosome
+  echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size"
+  
+  #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins)
+  nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/" 
+  #gives warning if no data in/for current chromosome
+  
+done
+
+#rm tmp
+rm $org_assembly_file
+