combine two files

Syed Tarique Moin · 07-02-2010, 09:03 AM

Hello,

i have two files with thousands of line, I am trying to combine these two files but i want to insert each line of one file to the another file after certain lines. I am using awk with the following command but it does not work.

cat file1 | awk ' { print $0; if (NR%3004==0) {print "file2"}}' > outputfile

Regards

David the H. · 07-02-2010, 09:18 AM

Please give us an example of the input file contents, and the desired output format. Also, what do you mean specifically by "it doesn't work"? It's very hard to give specific advice without knowing what we're working with.

grail · 07-02-2010, 09:30 AM

Also the 'cat' at the beginning is not required and you are simply printing the string "file2" at the chosen line, ie no contents.

David is correct though that a lot more information is needed prior to any real help being available.

Syed Tarique Moin · 07-02-2010, 11:34 AM

Hello,

Thanks for the reply, The example is as follows!

for example file 1

AAAAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
AAAAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
AAAAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
AAAAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
AAAAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
------------
------------
------------

File 2
111111111111111111111111111111111111111
222222222222222222222222222222222222222
333333333333333333333333333333333333333
444444444444444444444444444444444444444
----------------
---------------
----------------
-------------

I want to get out put like this

AAAAAAAAAAAAAABBBBBBBBBBBBBCCCCCCCCCCCC
111111111111111111111111111111111111111
AAAAAAAAAAAAAABBBBBBBBBBBBBCCCCCCCCCCCC
222222222222222222222222222222222222222
AAAAAAAAAAAAAABBBBBBBBBBBBBCCCCCCCCCCCC
333333333333333333333333333333333333333
AAAAAAAAAAAAAABBBBBBBBBBBBBCCCCCCCCCCCC
444444444444444444444444444444444444444

This is long file of the simulation trajectory. I want to put each different and consecutive line from file 2 to file 1 after specific lines e.g after every 50 lines.

Regards

grail · 07-02-2010, 11:57 AM

Well if using awk then this could help:

http://www.gnu.org/manual/gawk/html_...tline_002fFile

Syed Tarique Moin · 07-05-2010, 05:57 AM

Hello,

Thanks for the reply i have two files traj_H2O2.xyz and t.xyz, I want to insert each line of file t.xyz in another file traj_H2O2.xyz using the following command with get line.

cat traj_H2O2.xyz | awk ' { print $0; if (NR%3005==0) {getline $0 < "t.xyz"}}' > c.xyz

The output c.xyz is the same as the traj_H2O2.xyz.

Kindly i need guidance.

Regards

druuna · 07-05-2010, 06:12 AM

Hi,

Is this what you are looking for:

diff -y traj_H2O2.xyz t.xyz | sed 's/[[:blank:]][[:blank:]]*|[[:blank:]]/\n/' > c.xyz

Sample run:

Code:

$ cat traj_H2O2.xyz
A1AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
A2AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
A3AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
A4AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
A5AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC

$ cat t.xyz
111111111111111111111111111111111111111
222222222222222222222222222222222222222
333333333333333333333333333333333333333
444444444444444444444444444444444444444
555555555555555555555555555555555555555

$ diff -y traj_H2O2.xyz t.xyz | sed 's/[[:blank:]][[:blank:]]*|[[:blank:]]/\n/'
A1AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
111111111111111111111111111111111111111
A2AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
222222222222222222222222222222222222222
A3AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
333333333333333333333333333333333333333
A4AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
444444444444444444444444444444444444444
A5AAAAAAAAAAAA BBBBBBBBBBBBB CCCCCCCCCCCCCCC
555555555555555555555555555555555555555

Hope this helps.

Syed Tarique Moin · 07-05-2010, 07:56 AM

Hi,

Thanks for the reply. I don't want the difference of these file because these two files are not equal in numbers (of lines). It didn't work.

Regards

Syed Tarique Moin · 07-05-2010, 07:59 AM

It just puts every line of other file (file2) with every line of first file (file1) but i want to put the each line of a file (file2) into another file (file1) after specific interval then another line of file (file2) to another file (file1) after same specific interval.

Regards

druuna · 07-05-2010, 08:16 AM

Hi,

Output form your example (end post #4) looks like my output (end post #7).

I did change your input file a bit (second character is 1 to 5, to make sure the correct line is used).

If your example isn't what you want, then please post a relevant one......

How does this specific interval supposed to work/look?

Syed Tarique Moin · 07-05-2010, 08:35 AM

Thanks, I have a very large file. But i can give real input of my work below.

file 1
O -6.230600 3.314400 -12.287100
H -6.119800 3.047300 -11.368100
H -6.533100 4.204800 -12.096600
O 12.104800 2.198100 -15.244801
H 13.015100 2.087200 -15.000700
H 11.760301 2.773000 -14.558399
O 2.163200 14.690200 -12.447701
H 1.316700 14.269799 -12.596399
H 1.994400 15.476899 -13.053499
O 15.386072 6.185700 10.372772
H 14.869772 6.957000 10.262774
H -15.260300 6.326600 11.209572
O -0.915700 -6.342100 10.467173
H -0.108700 -6.814900 10.350771
H -1.477300 -6.455300 9.654371
O 6.318500 9.950600 2.828700
H 6.415500 8.971100 2.673700
H 7.237900 10.170699 2.589300

file2
Q 0.4402 -0.49655 -0.19745
Q 0.4392 -0.4938 -0.1963
Q 0.43845 -0.4914 -0.19525
Q 0.43775 -0.48955 -0.1947
Q 0.4373 -0.4882 -0.19495
Q 0.43705 -0.48725 -0.1964

output would be like this.

output
O -6.230600 3.314400 -12.287100
H -6.119800 3.047300 -11.368100
H -6.533100 4.204800 -12.096600
Q 0.4402 -0.49655 -0.19745
O 12.104800 2.198100 -15.244801
H 13.015100 2.087200 -15.000700
H 11.760301 2.773000 -14.558399
Q 0.4392 -0.4938 -0.1963
O 2.163200 14.690200 -12.447701
H 1.316700 14.269799 -12.596399
H 1.994400 15.476899 -13.053499
Q 0.43845 -0.4914 -0.19525
O 15.386072 6.185700 10.372772
H 14.869772 6.957000 10.262774
H -15.260300 6.326600 11.209572
Q 0.43775 -0.48955 -0.1947
O -0.915700 -6.342100 10.467173
H -0.108700 -6.814900 10.350771
H -1.477300 -6.455300 9.654371
Q 0.4373 -0.4882 -0.19495
O 6.318500 9.950600 2.828700
H 6.415500 8.971100 2.673700
H 7.237900 10.170699 2.589300
Q 0.43705 -0.48725 -0.1964

It shows that the both input file are different and each different line of file2 come after certain lines of file1. Its a short illustration but i have to put each different lines of file2 after specific interval of 3004 line of file 1.
I hope that this post would help you to understand my problem.
Regards

druuna · 07-05-2010, 09:04 AM

Hi again,

Another try

awk ' { print } NR % 3 == 0 { getline < "file2" ; print } ' file1

I guess you need to change 3 into 3004, but this seems to generate the example output given in post #11:

Code:

$ cat file1
O -6.230600 3.314400 -12.287100
H -6.119800 3.047300 -11.368100
H -6.533100 4.204800 -12.096600
O 12.104800 2.198100 -15.244801
H 13.015100 2.087200 -15.000700
H 11.760301 2.773000 -14.558399
O 2.163200 14.690200 -12.447701
H 1.316700 14.269799 -12.596399
H 1.994400 15.476899 -13.053499
O 15.386072 6.185700 10.372772
H 14.869772 6.957000 10.262774
H -15.260300 6.326600 11.209572
O -0.915700 -6.342100 10.467173
H -0.108700 -6.814900 10.350771
H -1.477300 -6.455300 9.654371
O 6.318500 9.950600 2.828700
H 6.415500 8.971100 2.673700
H 7.237900 10.170699 2.589300

$ cat file2
Q 0.4402 -0.49655 -0.19745
Q 0.4392 -0.4938 -0.1963
Q 0.43845 -0.4914 -0.19525
Q 0.43775 -0.48955 -0.1947
Q 0.4373 -0.4882 -0.19495
Q 0.43705 -0.48725 -0.1964

$ awk ' { print } NR % 3 == 0 { getline < "file2" ; print } ' file1
O -6.230600 3.314400 -12.287100
H -6.119800 3.047300 -11.368100
H -6.533100 4.204800 -12.096600
Q 0.4402 -0.49655 -0.19745
O 12.104800 2.198100 -15.244801
H 13.015100 2.087200 -15.000700
H 11.760301 2.773000 -14.558399
Q 0.4392 -0.4938 -0.1963
O 2.163200 14.690200 -12.447701
H 1.316700 14.269799 -12.596399
H 1.994400 15.476899 -13.053499
Q 0.43845 -0.4914 -0.19525
O 15.386072 6.185700 10.372772
H 14.869772 6.957000 10.262774
H -15.260300 6.326600 11.209572
Q 0.43775 -0.48955 -0.1947
O -0.915700 -6.342100 10.467173
H -0.108700 -6.814900 10.350771
H -1.477300 -6.455300 9.654371
Q 0.4373 -0.4882 -0.19495
O 6.318500 9.950600 2.828700
H 6.415500 8.971100 2.673700
H 7.237900 10.170699 2.589300
Q 0.43705 -0.48725 -0.1964

Hope this helps.

grail · 07-05-2010, 09:14 AM

druuna is on the money, it can be a little shorter but you get the drift:

Code:

awk '!(NR % 4){getline < "file2"}1' file1

Of course you need to redirect to new file.

druuna · 07-05-2010, 09:19 AM

@grail: Nice!

A bit unreadable (for the not so awk-savvy), but a very elegant solution!

grail · 07-05-2010, 09:33 AM

Quote:

A bit unreadable (for the not so awk-savvy)

Yeah my bad ... just like to play