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Regarding change in column numbers after some commands

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Top Forums Shell Programming and Scripting Regarding change in column numbers after some commands
# 1  
Old 11-08-2013
Regarding change in column numbers after some commands
Hi All,

I was using some commands to:
  1. replace a column by a constant string character
    Code:
     awk -v a=CA 'NF>1{ $3=a; print; } ' $line>$line"_1"

  2. to copy a column and paste it in another place
    Code:
     awk '$5=$2" "$5' $line>$line"_2"

  3. to delete the extra columns
    Code:
    awk '{for(i=1;i<=NF;i++) line=(i==1)?$i:((i==6)?line:line OFS $i);print line}' $line>$line"_3"

But by performing these sequence of functions, the columns of file format is changed which is not required.

Since, I need to use these files as input for running another code, and it is giving me the error just because the column numbers is changed.
Can anyone help me in doing these functions without changing the columns format.
# 2  
Old 11-08-2013
If you show input and expected output it would be better to help you.
# 3  
Old 11-08-2013
Initially, The file was like:
Code:
ATOM      1  N   LYS     1       3.440  10.397  -1.989  1.00 18.23
ATOM      2  CA  LYS     1       3.897  11.093  -3.203  1.00 17.09
ATOM      3  C   LYS     1       4.920  10.272  -3.962  1.00 16.14
ATOM      4  O   LYS     1       5.472   9.269  -3.488  1.00 15.98

after applying
Code:
awk -v a=CA 'NF>1{ $3=a; print; } ' $line>$line"_1"

for replacing N, C and O with CA the file was like:
Code:
ATOM 1 CA LYS 1 3.440 10.397 -1.989 1.00 18.23
ATOM 2 CA LYS 1 3.897 11.093 -3.203 1.00 17.09
ATOM 3 CA LYS 1 4.920 10.272 -3.962 1.00 16.14
ATOM 4 CA LYS 1 5.472 9.269 -3.488 1.00 15.98

Then, after applying
Code:
awk '$5=$2" "$5' $line>$line"_2"

for copy 2nd column and paste as a 5th column,we get:
Code:
ATOM 1 CA LYS 1 1 3.440 10.397 -1.989 1.00 18.23
ATOM 2 CA LYS 2 1 3.897 11.093 -3.203 1.00 17.09
ATOM 3 CA LYS 3 1 4.920 10.272 -3.962 1.00 16.14
ATOM 4 CA LYS 4 1 5.472 9.269 -3.488 1.00 15.98

Further, I applied
Code:
awk '{for(i=1;i<=NF;i++) line=(i==1)?$i:((i==6)?line:line OFS $i);print line}' $line>$line"_3"

for deleting the extra 6th column, and the output is like:
Code:
ATOM 1 CA LYS 1 3.440 10.397 -1.989 1.00 18.23
ATOM 2 CA LYS 2 3.897 11.093 -3.203 1.00 17.09
ATOM 3 CA LYS 3 4.920 10.272 -3.962 1.00 16.14
ATOM 4 CA LYS 4 5.472 9.269 -3.488 1.00 15.98

Actually, after all this modifications in my file, I need it to be like:
Code:
ATOM      1  CA   LYS     1       3.440  10.397  -1.989  1.00 18.23
ATOM      2  CA   LYS     2       3.897  11.093  -3.203  1.00 17.09
ATOM      3  CA   LYS     3       4.920  10.272  -3.962  1.00 16.14
ATOM      4  CA   LYS     4       5.472   9.269  -3.488  1.00 15.98

Please have a look at the column numbers and number of spaces between columns. After posting this reply, the number of spaces between the columns are showing same, but this is not the scene the blank space between ATOM and 1 is of 6 blank space in original file whereas it is only 1 after modifications.
Last edited by Don Cragun; 11-08-2013 at 07:43 AM.. Reason: Fix CODE tag.
# 4  
Old 11-08-2013
That's because awk treats any number of spaces as field separator (unless told otherwise). As you can see, the formatting has already gone in the first action's output. If you need exactly formatted output, use printf for all the fields.
This User Gave Thanks to RudiC For This Post:
CAch
# 5  
Old 11-08-2013
Hi RudiC,

Thanks for your reply.
I actually dont know the use of printf in shell script. can you plz giv e me a format by which I can convert my awk commands in printf form
# 6  
Old 11-08-2013
man printf

In your case, start with printf "%-9s%-3s\n", $1, $2 and then expand.
# 7  
Old 11-08-2013
I tried this one:
Code:
gawk '{print $1,"     ", $2," ",$3," ",$4,"  ",$5,"     ",$6,"",$7,"",$8,"",$9,"",$10}' $line>new

After this I am getting:

Code:
ATOM       1   CA   LYS    1       4.816  8.341  0.644  1.00  0.18
ATOM       2   CA   LYS    2       4.790  8.614  -0.804  1.00  0.00
ATOM       3   CA   LYS    3       4.989  10.100  -1.068  1.00  0.83
ATOM       4   CA   LYS    4       3.902  10.937  -0.409  1.00  1.35
ATOM       5   CA   LYS    5       4.120  12.421  -0.673  1.00  1.50
ATOM       6   CA   LYS    6       3.037  13.264  -0.007  1.00  1.72
ATOM       7   CA   LYS    7       3.250  14.696  -0.268  1.00  1.92
ATOM       8   CA   LYS    8       5.891  7.843  -1.514  1.00  0.05
ATOM       9   CA   LYS    9       6.558  6.986  -0.925  1.00  0.17
ATOM       10   CA   SER    10       6.078  8.168  -2.782  1.00  0.03
ATOM       11   CA   SER    11       7.151  7.551  -3.567  1.00  0.00
ATOM       12   CA   SER    12       6.995  7.953  -5.030  1.00  0.15
ATOM       13   CA   SER    13       7.629  9.216  -5.194  1.00  0.08
ATOM       14   CA   SER    14       8.489  8.067  -3.059  1.00  0.07

But now, I need to right align the columns. For which I again tried printf command, which is not working for entire file columns and for multiple files in script.
Can you plz help me in finding a way to right justify the columns for multiple files.
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