Split single file into multiple files based on the number in the column

Shell Programming and Scripting
1

Dear All,

I would like to split a file of the following format into multiple files based on the number in the 6th column (numbers 1, 2, 3...):

ATOM      1  N   GLY A   1      -3.198  27.537  -5.958  1.00  0.00           N  
ATOM      2  CA  GLY A   1      -2.199  28.399  -6.617  1.00  0.00           C  
ATOM      3  C   GLY A   1      -2.168  29.706  -5.855  1.00  0.00           C  
ATOM      4  O   GLY A   2      -3.205  30.358  -5.782  1.00  0.00           O  
ATOM      5  H1  GLY A   2      -3.280  26.649  -6.428  1.00  0.00           H  
ATOM      6  HA2 GLY A   3      -1.220  27.923  -6.579  1.00  0.00           H  
ATOM      7  HA3 GLY A   3      -2.492  28.588  -7.649  1.00  0.00           H  
ATOM      8  N   SER A   3      -1.051  30.010  -5.194  1.00  0.00           N  
ATOM      9  CA  SER A   4      -1.141  30.319  -3.777  1.00  0.00           C  
ATOM     10  C   SER A   4       0.107  31.009  -3.229  1.00  0.00           C  
ATOM     11  O   SER A   5       1.081  31.273  -3.935  1.00  0.00           O  
ATOM     12  CB  SER A   5      -1.242  29.003  -2.978  1.00  0.00           C  
ATOM     13  OG  SER A   5      -2.210  28.079  -3.427  1.00  0.00           O  
ATOM     14  H   SER A   5      -0.165  29.571  -5.395  1.00  0.00           H  
ATOM     15  HA  SER A   5      -2.021  30.936  -3.581  1.00  0.00           H  
ATOM     16  HB2 SER A   6      -0.271  28.504  -2.981  1.00  0.00           H  
ATOM     17  HB3 SER A   6      -1.481  29.244  -1.942  1.00  0.00           H

I would like to get separate files based on the information in the 6th column:

File 1:

ATOM      1  N   GLY A   1      -3.198  27.537  -5.958  1.00  0.00           N  
ATOM      2  CA  GLY A   1      -2.199  28.399  -6.617  1.00  0.00           C  
ATOM      3  C   GLY A   1      -2.168  29.706  -5.855  1.00  0.00           C  
ATOM      4  O   GLY A   2      -3.205  30.358  -5.782  1.00  0.00           O  
ATOM      5  H1  GLY A   2      -3.280  26.649  -6.428  1.00  0.00           H  

File 2:

ATOM      4  O   GLY A   2      -3.205  30.358  -5.782  1.00  0.00           O  
ATOM      5  H1  GLY A   2      -3.280  26.649  -6.428  1.00  0.00           H  
ATOM      6  HA2 GLY A   3      -1.220  27.923  -6.579  1.00  0.00           H  
ATOM      7  HA3 GLY A   3      -2.492  28.588  -7.649  1.00  0.00           H  
ATOM      8  N   SER A   3      -1.051  30.010  -5.194  1.00  0.00           N  

File 3:

ATOM      6  HA2 GLY A   3      -1.220  27.923  -6.579  1.00  0.00           H  
ATOM      7  HA3 GLY A   3      -2.492  28.588  -7.649  1.00  0.00           H  
ATOM      8  N   SER A   3      -1.051  30.010  -5.194  1.00  0.00           N  
ATOM      9  CA  SER A   4      -1.141  30.319  -3.777  1.00  0.00           C  
ATOM     10  C   SER A   4       0.107  31.009  -3.229  1.00  0.00           C  

File 4:

ATOM      9  CA  SER A   4      -1.141  30.319  -3.777  1.00  0.00           C  
ATOM     10  C   SER A   4       0.107  31.009  -3.229  1.00  0.00           C  
ATOM     11  O   SER A   5       1.081  31.273  -3.935  1.00  0.00           O  
ATOM     12  CB  SER A   5      -1.242  29.003  -2.978  1.00  0.00           C  
ATOM     13  OG  SER A   5      -2.210  28.079  -3.427  1.00  0.00           O  
ATOM     14  H   SER A   5      -0.165  29.571  -5.395  1.00  0.00           H  
ATOM     15  HA  SER A   5      -2.021  30.936  -3.581  1.00  0.00           H  

File 5:

ATOM     11  O   SER A   5       1.081  31.273  -3.935  1.00  0.00           O  
ATOM     12  CB  SER A   5      -1.242  29.003  -2.978  1.00  0.00           C  
ATOM     13  OG  SER A   5      -2.210  28.079  -3.427  1.00  0.00           O  
ATOM     14  H   SER A   5      -0.165  29.571  -5.395  1.00  0.00           H  
ATOM     15  HA  SER A   5      -2.021  30.936  -3.581  1.00  0.00           H  
ATOM     16  HB2 SER A   6      -0.271  28.504  -2.981  1.00  0.00           H  
ATOM     17  HB3 SER A   6      -1.481  29.244  -1.942  1.00  0.00           H

I would be very grateful if you could please write me a few lines of bash/awk/sed/csplit code that goes through the file and outputs multiple files. The file format given above (PDB) is used to describe 3D protein structures.

I thank you for your help in advance.

Thanks,
Tomas

2

Hi,

You have mentioned

...multiple files based on the number in the 6th column (numbers 1, 2, 3...):..

But your expected output looks different.

Do you mean this ?

$ awk '{close(f);f=$6}{print > f".txt"}' input.txt

$ cat 1.txt
ATOM      1  N   GLY A   1      -3.198  27.537  -5.958  1.00  0.00           N
ATOM      2  CA  GLY A   1      -2.199  28.399  -6.617  1.00  0.00           C
ATOM      3  C   GLY A   1      -2.168  29.706  -5.855  1.00  0.00           C

$ cat 2.txt
ATOM      4  O   GLY A   2      -3.205  30.358  -5.782  1.00  0.00           O
ATOM      5  H1  GLY A   2      -3.280  26.649  -6.428  1.00  0.00           H

Hope this helps.

3 
awk '{print > ("file" $6)}' infile

..see previous answer :wink:

4 
$ awk '{var=$6; var=var-1} {print >"file"$6} {print >"file"var}' urfile

$ cat file1
ATOM      1  N   GLY A   1      -3.198  27.537  -5.958  1.00  0.00           N
ATOM      2  CA  GLY A   1      -2.199  28.399  -6.617  1.00  0.00           C
ATOM      3  C   GLY A   1      -2.168  29.706  -5.855  1.00  0.00           C
ATOM      4  O   GLY A   2      -3.205  30.358  -5.782  1.00  0.00           O
ATOM      5  H1  GLY A   2      -3.280  26.649  -6.428  1.00  0.00           H