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Remove the first character from the fourth column only if the column has four characters

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# 1  
Old 08-13-2013
Remove the first character from the fourth column only if the column has four characters
I have a file as follows

Code:
ATOM   5181  N  AMET K 406      12.440   6.552  25.691  0.50  7.37           N   
ATOM   5182  CA AMET K 406      13.685   5.798  25.578  0.50  5.87           C   
ATOM   5183  C  AMET K 406      14.045   5.179  26.909  0.50  5.07           C   
ATOM   5184  O   MET K 406      14.595   4.083  27.003  0.50  7.07           O   
ATOM   5185  CB  MET K 406      14.812   6.674  25.044  0.50  6.80           C   
ATOM   5191  C  BMET K 406      14.044   5.177  26.910  0.50  5.15           C   
ATOM   5192  O  BMET K 406      14.589   4.078  27.004  0.50  7.09           O  
ATOM   5197  N   ALA K 407      13.718   5.884  27.972  1.00  5.30           N   
ATOM   5198  CA  ALA K 407      14.077   5.408  29.309  1.00  6.16           C 
ATOM   5202  N  AARG K 408      12.186   3.982  29.147  0.50  6.55           N   
ATOM   5203  CA AARG K 408      11.407   2.745  29.387  0.50  7.31           C

I would like to remove the first character from the fourth column only if the column has four characters. (in-place editing)

Desired output

Code:
ATOM   5181  N   MET K 406      12.440   6.552  25.691  0.50  7.37           N   
ATOM   5182  CA  MET K 406      13.685   5.798  25.578  0.50  5.87           C   
ATOM   5183  C   MET K 406      14.045   5.179  26.909  0.50  5.07           C   
ATOM   5184  O   MET K 406      14.595   4.083  27.003  0.50  7.07           O   
ATOM   5185  CB  MET K 406      14.812   6.674  25.044  0.50  6.80           C   
ATOM   5191  C   MET K 406      14.044   5.177  26.910  0.50  5.15           C   
ATOM   5192  O   MET K 406      14.589   4.078  27.004  0.50  7.09           O  
ATOM   5197  N   ALA K 407      13.718   5.884  27.972  1.00  5.30           N   
ATOM   5198  CA  ALA K 407      14.077   5.408  29.309  1.00  6.16           C 
ATOM   5202  N   ARG K 408      12.186   3.982  29.147  0.50  6.55           N   
ATOM   5203  CA  ARG K 408      11.407   2.745  29.387  0.50  7.31           C

# 2  
Old 08-13-2013
You could use substr in awk:

Code:
awk '{ print substr($0,1,16) " " substr($0,18) }' infile

# 3  
Old 08-13-2013
Thanks for your answer. I need in-place editing. Is it possible?
# 4  
Old 08-13-2013
Hello,

Could you please try the following and let me know if this helps you.


1st code is as follows.

Code:
sed 's/.MET/MET/g; s/.ARG/ARG/g' remove_char_4th_column

Output will be as folllows.

Code:
ATOM   5181  N  MET K 406      12.440   6.552  25.691  0.50  7.37           N
ATOM   5182  CA MET K 406      13.685   5.798  25.578  0.50  5.87           C
ATOM   5183  C  MET K 406      14.045   5.179  26.909  0.50  5.07           C
ATOM   5184  O  MET K 406      14.595   4.083  27.003  0.50  7.07           O
ATOM   5185  CB MET K 406      14.812   6.674  25.044  0.50  6.80           C
ATOM   5191  C  MET K 406      14.044   5.177  26.910  0.50  5.15           C
ATOM   5192  O  MET K 406      14.589   4.078  27.004  0.50  7.09           O
ATOM   5197  N   ALA K 407      13.718   5.884  27.972  1.00  5.30           N
ATOM   5198  CA  ALA K 407      14.077   5.408  29.309  1.00  6.16           C
ATOM   5202  N  ARG K 408      12.186   3.982  29.147  0.50  6.55           N
ATOM   5203  CA ARG K 408      11.407   2.745  29.387  0.50  7.31           C


2nd code is as follows.

Code:
sed 's/AMET/MET/g; s/BMET/MET/g; s/AARG/ARG/g' remove_char_4th_column


Output will be as follows.


Code:
ATOM   5181  N  MET K 406      12.440   6.552  25.691  0.50  7.37           N
ATOM   5182  CA MET K 406      13.685   5.798  25.578  0.50  5.87           C
ATOM   5183  C  MET K 406      14.045   5.179  26.909  0.50  5.07           C
ATOM   5184  O   MET K 406      14.595   4.083  27.003  0.50  7.07           O
ATOM   5185  CB  MET K 406      14.812   6.674  25.044  0.50  6.80           C
ATOM   5191  C  MET K 406      14.044   5.177  26.910  0.50  5.15           C
ATOM   5192  O  MET K 406      14.589   4.078  27.004  0.50  7.09           O
ATOM   5197  N   ALA K 407      13.718   5.884  27.972  1.00  5.30           N
ATOM   5198  CA  ALA K 407      14.077   5.408  29.309  1.00  6.16           C
ATOM   5202  N  ARG K 408      12.186   3.982  29.147  0.50  6.55           N
ATOM   5203  CA ARG K 408      11.407   2.745  29.387  0.50  7.31           C


Where I am having the input provided bby you in a file named remove_char_4th_column.



Thanks,
R. Singh
# 5  
Old 08-13-2013
Hi Ravinder singh,

Thank you for your answer. I need in-place editing because I have lot of files like this. In the given example, the name of strings are AMET, BMET, AARG and ALA. In other files, the name of strings are different. So I think, your code is difficult for me to use for multiple files.
# 6  
Old 08-13-2013
If the format is fixed the solution from Chubler should work.
To edit the file do
Code:
awk '{ print substr($0,1,16) " " substr($0,18) }' orgfile > newfile ; mv newfile orgfile

This will replace the file, (same as sed -i), not sure if you can do it in an other way.
# 7  
Old 08-13-2013
Inline change...
Try this... Works for the given pattern...
Code:
sed -i 's/\(.* \).*\(... [A-Z] [0-9].*\)/\1\2/g' infile

Code:
-bash-3.2$ sed 's/\(.* \).*\(... [A-Z] [0-9].*\)/\1\2/g' infile
ATOM   5181  N  MET K 406      12.440   6.552  25.691  0.50  7.37           N
ATOM   5182  CA MET K 406      13.685   5.798  25.578  0.50  5.87           C
ATOM   5183  C  MET K 406      14.045   5.179  26.909  0.50  5.07           C
ATOM   5184  O   MET K 406      14.595   4.083  27.003  0.50  7.07           O
ATOM   5185  CB  MET K 406      14.812   6.674  25.044  0.50  6.80           C
ATOM   5191  C  MET K 406      14.044   5.177  26.910  0.50  5.15           C
ATOM   5192  O  MET K 406      14.589   4.078  27.004  0.50  7.09           O
ATOM   5197  N   ALA K 407      13.718   5.884  27.972  1.00  5.30           N
ATOM   5198  CA  ALA K 407      14.077   5.408  29.309  1.00  6.16           C
ATOM   5202  N  ARG K 408      12.186   3.982  29.147  0.50  6.55           N
ATOM   5203  CA ARG K 408      11.407   2.745  29.387  0.50  7.31           C

Pattern is built assuming there will be a single alphabet (here it is K) followed by a space and a number.

--ahamed
Last edited by ahamed101; 08-13-2013 at 05:27 AM..
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