/cistromescripts/batch_faToNib.sh

https://bitbucket.org/cistrome/cistrome-harvard/ · Shell · 12 lines · 10 code · 1 blank · 1 comment · 2 complexity · 8e98ba988e01c5987159bc35d353b544 MD5 · raw file 

    

  1. #!/bin/bash
    2. 

  2. 

  3. for i in `ls */raw*/*.fa`;do
    4. 

  4.     DRAW=`dirname $i`;
    5. 

  5.     FRAW=`basename $i`;
    6. 

  6.     DNIB=${DRAW%\/*}/nib/;
    7. 

  7.     if [ ! -d $DNIB ];then
    8. 

  8.         mkdir $DNIB;
    9. 

  9.     fi
    10. 

  10.     FNIB=${FRAW/.fa/.nib};
    11. 

  11.     faToNib -softMask $i ${DNIB}${FNIB};
    12. 

  12. done
    13.