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Full Discussion: Regarding change in column numbers after some commands
Top Forums Shell Programming and Scripting Regarding change in column numbers after some commands Post 302872253 by CAch on Friday 8th of November 2013 04:40:31 AM
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.
 

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