Shell Programming and Scripting

A1  data
B1 data
C1 data

A2 data
B2 data
C2 data

A1,data
A2,data
A3,data
B1,data
B2,data
B3,data
...

A1,data,B1,data,C1,data
A2,data,B2,data,C2,data
A3,data,B3,data,C3,data

#!/bin/bash
#ATR Kinetic Analysis Script for KDE
#author: ParadoxDruid
#created March 13, 2008
#modified August 6th, 2008

#say hello
kdialog --msgbox "Signalyze ATR Data Converter\nPress OK to select working directory"
#navigate to proper directory
DIRECTORY=`kdialog --getexistingdirectory .`
#get necessary info from user
NAME=`kdialog --title "Trial Name" --inputbox "Name of your trial"`
echo $NAME" Trial Set" > $DIRECTORY/$NAME.csv
echo -e "Seq,Point,Integral,sd" >> $DIRECTORY/$NAME.csv
#filename set
SET=`kdialog --title "Sets" --inputbox "What is the name of your results files? (i.e.  kinetics-1_  )"`
#end filename set

#probe sequence detection
cat $DIRECTORY/"$SET"1.stx | sed '1,22d' > $DIRECTORY/$NAME.temp
SEQNUM=`cat $DIRECTORY/$NAME.temp | wc -l`
#end probe sequence detection

#data points auto-detection
POINTS=`ls $DIRECTORY | grep $SET | grep stx | sed 's/'$SET'//' | sed 's/\.stx//' | sort -n | tail -n1`
#end data points auto detection

#probe names routine
for ((c=1;c<$SEQNUM+1;c++)); do
sequences[$c]=`cat $DIRECTORY/$NAME.temp | head -n$c | tail -n1 | cut -f 1`
done
#end routine

#increment the number of data points, since the ATR doesn't use 0
let "TRIALS=$POINTS+1"

#define a function to grab data
seqgrab() {
for ((i=1;i<$TRIALS;i++)); do
data=`cat $DIRECTORY/"$SET"$i.stx | grep -w $1 | cut -f 5`
sd=`cat $DIRECTORY/"$SET"$i.stx | grep -w $1 | cut -f 6`
 echo -e $1 "," $i "," $data "," $sd  >> $DIRECTORY/$NAME.csv
done
}

#tell about our progress
dcopRef=`kdialog --progressbar "Initialising" ${#sequences[@]}`

#iterate through the data files
for ((n=1;n<${#sequences[@]}+1;n++)); do
seqgrab ${sequences[${n}]}
dcop $dcopRef setProgress $n
dcop $dcopRef setLabel "Working..."
done

rm $DIRECTORY/$NAME.temp
dcop $dcopRef close
kdialog --textbox $DIRECTORY/$NAME.csv 440 800
exit 0

Time 6
Probe_Name    Count    Net_Signal    Net_Signal_SD    Net_Integral    Net_Integral_SD    Proc_Control    
A1    5    0.04594    0.01175    0.81596    0.23182    OK    
B1    3    0.02464    0.00381    0.59647    0.15367    OK    
C1    5    0.13487    0.02862    2.54441    0.29700    OK

Time 7
Probe_Name    Count    Net_Signal    Net_Signal_SD    Net_Integral    Net_Integral_SD    Proc_Control    
A1    5    0.04545    0.01211    0.82307    0.24171    OK    
B1    3    0.02332    0.00557    0.56161    0.10771    OK    
C1    5    0.13672    0.02963    2.54276    0.26535    OK    
D1    5    0.14061    0.07675    2.58301    1.31850    OK

Seq,Point,Integral,sd
A1 ,1,0.81596,0.23182
A1 ,2,0.81793,0.2443
A1 ,3,0.82073,0.24254
A1 ,4,0.82307,0.24171
A1 ,5,0.81935,0.23554
B1 ,1,0.59647,0.15367
B1 ,2,0.57585,0
B1 ,3,0.55278,0.11597
B1 ,4,0.56161,0.10771
B1 ,5,0.49331,0.08419
C1 ,1,2.54441,0.297

paste -s file1 file2 file3 ... | tr '\t' ','

A1(time 1) and all numerical fields
B1(time 1) and all numerical fields
...

A1(time 2) and all numerical fields
B1(time 2) and all numerical fields
...

A1(time 1) and fields 5 and 6,B1(time 1) and fields 5 and 6, C1(time 1) and fields 5 and 6,...
A1(time 2) and fields 5 and 6,B1(time 2) and fields 5 and 6, C1(time 2) and fields 5 and 6,... 
...

paste -d"|" file1 file2 file3 | tr "|" "\n"