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

Shell Programming and Scripting
1

I have a file as follows

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

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

You could use substr in awk:

awk '{ print substr($0,1,16) " " substr($0,18) }' infile
3

Thanks for your answer. I need in-place editing. Is it possible?

4

Hello,

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

1st code is as follows.

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

Output will be as folllows.

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.

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

Output will be as follows.

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

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

If the format is fixed the solution from Chubler should work.
To edit the file do

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

Inline change...
Try this... Works for the given pattern...

sed -i 's/\(.* \).*\(... [A-Z] [0-9].*\)/\1\2/g' infile

-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

8

@ahamed
You remove to much with this. Column 4 should be at least 3 characters long.
You have 2 in row 4,5,8,9

@hasanabdulla
Is format always the same in all the file? Then use Chublers solution
Are there other combination of letters than MET ALA ARG ? Then do not use sed solution that just replace text

9

oh yeah, I didn't notice that.

--ahamed

---------- Post updated at 12:11 AM ---------- Previous update was at 12:08 AM ----------

Corrected the code in post#5

--ahamed

10

This test if field 4 has more than 3 characters, if it does, remove the first character.
Not sure why it mess up the format and how to fix it.

awk  '{$4=(length($4)>3)?substr($4,2):$4}1' file
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
11

Hi,
My file is seperated with ";" delimiter, after 13 delimiter i want to put the data in new line...

eg:
My current file:-

a;b;c;d;e;f;g;h;e;f;h;s;t;a;i;o;q;t;q;r;yu;f;sz;f;t;r...........

i want o/p as:-

a;b;c;d;e;f;g;h;e;f;h;s;t
a;i;o;q;t;q;r;yu;f;sz;f;t;r

How to achieve ths,
Please help me out in this...let me know if require any other info
thanks,

12

Start a new thread with you question

13 
awk '{$4=substr($4,length($4)-2)}1' file
14 
sed -i 's/^\(\([^[:space:]]\{1,\}[[:space:]]\{1,\}\)\{3\}\)[^[:space:]]\([^[:space:]]\{3\}\)/\1 \3/' file

NB the -i option is specific to GNU sed.
With a standard sed, use the following:

cp file file.old &&
sed '...' &&
rm -f file.old

Or use perl! (looks nicer anyway)

perl -i -pe 's/^((\S+\s+){3})\S(\S{3})/$1 $3/' file
15

Another option:

sed -i.bak 's/./ /17' file