Shell Programming and Scripting

#!/bin/ksh
inputfile=/tmp/myfile.input
outputfile=/tmp/myfile.output

for sample in `sort -n +1 $inputfile|cut -f1 -d","`
do
   echo "\n${sample} \c"              # Start new output record
   for mirna in `grep "^${sample}," $inputfile | cut -f2 -d "," | sort -n`
   do
      line=`grep "^${sample}, ${mirna}," $inputfile"`
      rpm="${line##*,}"                  # Get last field based on comma separator
      echo "${mirna} \c"                  # Append but do not end output record
   done
done >> $outputfile

#!/bin/ksh
inputfile=/tmp/myfile.input
outputfile=/tmp/myfile.output
typeset -i max_sample max_mirna RPM
read max_sample?"How many samples? "
read max_mirna?"How many mirna? "

{
echo "Sample, \c"
mirna=1
while [ $mirna -le $max_mirna ]
do
   echo "miRNA${mirna}, \c"           # Build up title line
   ((mirna=$mirna+1))
done

# Now process the data records
sample=1
while [ $sample -le $max_sample ]
do
   echo "\n${sample},\c"              # Start new line
   mirna=1
   while [ $mirna -le $max_mirna ]
   do
      line=`grep "^Sample${sample}, mirna${mirna}, " $inputfile`
      RPM="${line##*,}"               # Get last field only
      echo "${RPM},\c"
      ((mirna=$mirna+1))
   done
   ((sample=$sample+1))
done ; echo                           # Complete last record
} > $outputfile

awk -F, '{
   v = $2
   gsub(/[aA-zZ ]/, "", v)
   if (!x[$1])
      x[$1] = $1
   n = split(x[$1], a, " ") 
   a[v+2] = $NF
   x[$1] = ""
   for (i=1; i<=v+2; i++)
      x[$1] = sprintf("%s%s ", x[$1] ? x[$1] : "", a[i] ? a[i] : 0)
} END {for (i in x) print x[i]}' file

awk -F, '{
   v = $2
   gsub(/[aA-zZ ]/, "", v)
   if (!x[$1])
      x[$1] = $1
   n = split(x[$1], a, " ")
   a[v+2] = $NF+0
   x[$1] = ""
   v = (v < n ? n : v+2)
   for (i=1; i<=v; i++)
      x[$1] = sprintf("%s%s%s", x[$1] ? x[$1] : "", a[i] ? a[i] : 0, i < v ? " " : "")
} END {
   for (i in x) {
      gsub(" ", ",", x[i])
      sub(",", " ", x[i])
      print x[i]
   }
}' file