/cistromescripts/batch_faToNib.sh

 1#!/bin/bash
 2
 3for i in `ls */raw*/*.fa`;do
 4    DRAW=`dirname $i`;
 5    FRAW=`basename $i`;
 6    DNIB=${DRAW%\/*}/nib/;
 7    if [ ! -d $DNIB ];then
 8        mkdir $DNIB;
 9    fi
10    FNIB=${FRAW/.fa/.nib};
11    faToNib -softMask $i ${DNIB}${FNIB};
12done