Utility script to create bigWig files from phastCons wig data files. Needs the chromosome sizes which can be obtained by doing e. "fetchChromSizes mm9 > mm9chromSizes". For each .data file in the specified directory, runs wigToBigWig to generate corresponding .bw file.

make_bw_files.sh

#!/bin/sh
#
CHROMSIZE_FILE=$1
if [ -z "$CHROMSIZE_FILE" ] ; then
    echo "Usage: $0 CHROMSIZE_FILE [ DATA_DIR ]"
    exit
fi
if [ -z "$2" ] ; then
    DATA_DIR=`pwd`
else
    DATA_DIR=$2
fi
data_files=`ls $DATA_DIR/*.data`
for f in $data_files ; do
    echo $f
    bw=`basename $f`
    bw=${bw%.*}.bw
    if [ -f "$bw" ] ; then
	echo "$bw already exists"
    else
	wigToBigWig -clip $f $CHROMSIZE_FILE $bw
	if [ ! -f "$bw" ] ; then
	    echo "Failed to make $bw"
	    exit
	fi
    fi
done
##
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