UNIX for Dummies Questions & Answers

for i in /home/user/ABCD/*
do
FNAME=$(basename ${i})
FPATH=$(dirname ${i})
DNAME=${basename ${FNAME})
mv ${i} ${FPATH}/${DNAME}.${FNAME}
done

for file in /path/to/your/directory/*
do
  fname=${file##*/} #This gives your base filename.
  fpath=${file%/*} # Your dir
  dname=${fpath##*/}
  mv $file ${fpath}/${dname}.${fname}
done

cur_dir=`pwd`
for loop_dir in `ls -altr | awk '{if($9!="." && $9!=".." && $9!="")print $9}'`
do
cd $cur_dir
if [ -d $loop_dir ] ; then
cd $cur_dir/$loop_dir 
for loop_files in `ls -altr | awk '{if($9!="." && $9!=".." && $9!="")print $9}'`
do
if [ -f $loop_files ] ; then
mv $loop_files $loop_dir.$loop_files
fi
done
fi
done

for i in $(ls); do                        # runs through the 'items' in this dir                               
  if [ -d $i ]; then                      # if this is a dir
     fname=${i##*/}                 # pick up the dir name which will be used as prefix
     echo $fname                           
     cd $i                                    # move into the dir       
     for z in test*.fq; do               # loop over files starting with test and fq extension
       echo $z  
       cp $z ${fname}.${z}         # put the prefix to the file.               
     done                                        
     cd ..                                         
  fi                                              
done