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# 1  
Old 06-25-2007
pls help
Hi,
I need your help guys. I have two data files, namely 101.amberized.pdb & 101.pdb .

Now I want to replace the whole 3rd column of 101.amberized.pdb with the 3rd column of 101.pdb file. How do I do it in shell?
Thanks in advance

Parimal
# 2  
Old 06-25-2007
You can use join command if you have common fields. Else show your input files?
# 3  
Old 06-25-2007
Bug pls help
Dear Parimal,
if you want to replace only 3rd column then,
first use sed command like,

#!/bin/sh
var1=`sed -n '3p' 101.pdb `
var2=`sed -n '3p' 101.amberized.pdb`

sed -n 's/$var2/$var1/' 101.amberized.pdb >> outfile.txt

gud luk...
# 4  
Old 06-25-2007
Panknil,
The '3p' option in the "sed" command will print the third line/record
in the file, not the third column in each record.
As Anbu said, we need a sample of both files to find a solution.
# 5  
Old 06-25-2007
Bug pls help
Dear Shelllife,
initially i made mistake to understand the requirement,

if he wants to replace the 3rd column then he can use,

#!/bin/sh
var1=`awk -F 'FS' '{print $3}' 101.pdb`
var2=`awk -F 'FS' '{print $3}' 101.amberized.pdb`
sed -n 's/$var2/$var1/g' 101.amberized.pdb >> outfile.txt

*FS= Field Seperator
it will work...
Gud luk
# 6  
Old 06-25-2007
awk+sed
I think you can do as follow:
Suppose the content of fir is
a b c
d e f
the content of sec is
A B C
D E F

THEN,
i=1
while read line
do
t=`awk '{if(NR=="'"$i"'") print $2}' sec`
tt=`echo $line | awk '{print $2}'`
echo $line | sed "s/$tt/$t"
let i=i+1
done < fir

Then the output will be
a B c
d E f

Hope this will be what you desired
Smilie
# 7  
Old 06-25-2007
Quote:
Originally Posted by panknil
Dear Shelllife,
initially i made mistake to understand the requirement,

if he wants to replace the 3rd column then he can use,

#!/bin/sh
var1=`awk -F 'FS' '{print $3}' 101.pdb`
var2=`awk -F 'FS' '{print $3}' 101.amberized.pdb`
sed -n 's/$var2/$var1/g' 101.amberized.pdb >> outfile.txt

*FS= Field Seperator
it will work...
Gud luk
Dear friend panknil,
you'll need to re-read both the original post and the 'man awk'. You'll also need to brush up on the differences between the double-quotes and the single-quotes in shells.
101.pdb:
Code:
a b c
d e f

101.amberized.pdb
Code:
A B C
D E F

nawk -f chuchu.awk 101.pdb 101.amberized.pdb

chuchu.awk:
Code:
FNR==NR { arr[FNR]=$3; next}
{ $3=arr[FNR];print}

Last edited by vgersh99; 06-25-2007 at 11:43 AM..
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