Join multiple files by column with awk Post: 302427218

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Top Forums Shell Programming and Scripting Join multiple files by column with awk Post 302427218 by ikki on Friday 4th of June 2010 08:19:25 AM

06-04-2010

Registered User

awk is not necessary for this task

If you don't have to use awk, the result you ask for can perhaps be achieved using basic shell tools and sed.

Eg. if the files are called file1, file2 and file3 and have the headers stripped off you could achieve the desired result this way:

Code:

$ cat file1
cnvi0000001 5 164388439 -0.4241 0.0097
cnvi0000002 5 165771245 0.4448 1
cnvi0000003 5 165772271 0.4321 0
cnvi0000004 5 166325838 0.0403 0.9971
cnvi0000005 5 166710354 0.2355 0
$ cat file2
cnvi0000001 5 164388439 0.0736 0
cnvi0000002 5 165771245 0.1811 1
cnvi0000003 5 165772271 0.2955 0.0042
cnvi0000004 5 166325838 -0.118 0.9883
$ cat file3
cnvi0000001 5 164388439 0.2449 0
cnvi0000002 5 165771245 -0.0163 1
cnvi0000003 5 165772271 0.3361 0
cnvi0000004 5 166325838 0.0307 0.9867
cnvi0000005 5 166710354 0.1529 0
$ paste file* | sed -e 's/\t\t/\t     /g;s/\t/ /g;s/ /\t/g' | cut  -f 2,3,4,9,14
5       164388439       -0.4241 0.0736  0.2449
5       165771245       0.4448  0.1811  -0.0163
5       165772271       0.4321  0.2955  0.3361
5       166325838       0.0403  -0.118  0.0307
5       166710354       0.2355          0.1529

This assumes that the fields in file1, file2 and file3 are separated with spaces. If they are sepatared by tabs, the sed command has to be modified so it prints tabs instead of spaces, but I didn't test it.

EDIT: You should post more details of the data you need to manipulate. For example, if more than one files are shorter than the others, the above will not work reliably. Also, is it possible that some records are skipped? For example a line starting with cnvi0000004 is immediately followed by a line starting with cnvi0000006. The best solution in my opinion would be to preprocess the files so they are of equal length of lines, and insert "empty" data for missing fields, eg. "-".

EDIT2: A more robust sed command handling possible consecutive empty records:

Code:

$ paste file* file2 file2 file3 | sed -e 's/\([^\t]\)\t/\1 /g;s/\t/     /g;s/\t/ /g;s/ /\t/g' | cut  -f 2,3,4,9,14,19,24,29
5       164388439       -0.4241 0.0736  0.2449  0.0736  0.0736  0.2449
5       165771245       0.4448  0.1811  -0.0163 0.1811  0.1811  -0.0163
5       165772271       0.4321  0.2955  0.3361  0.2955  0.2955  0.3361
5       166325838       0.0403  -0.118  0.0307  -0.118  -0.118  0.0307
5       166710354       0.2355          0.1529                  0.1529

Last edited by ikki; 06-04-2010 at 10:11 AM.. Reason: addemdum

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diff3

diff3(1)						      General Commands Manual							  diff3(1)

NAME

       diff3 - 3-way differential file comparison

SYNOPSIS

       file1 file2 file3

DESCRIPTION

       compares three versions of a file, and prints disagreeing ranges of text flagged with these codes:

	      all three files differ
	      file1	is different
	      file2	is different
	      file3	is different

       The type of change required to convert a given range of a given file to some other is indicated in one of these ways:

	      Text is to be appended after line number
			     n1 in file f, where f = or

	      Text is to be changed in the range line
			     n1 through line n2.  If n1 = n2, the range can be abbreviated to n1.

       The  original  contents of the range follows immediately after a indication.  When the contents of two files are identical, the contents of
       the lower-numbered file is suppressed.

	      Produces a script for the
			editor that can be used to incorporate into file1 all changes between file2 and file3 (see ed(1)); i.e., the changes  that
			normally would be flagged and

	      Produces a script to incorporate only changes flagged

	      Produces a script to incorporate only changes flagged

	      Produces a script that will incorporate all
			changes  between  file2  and  file3,  but treat overlapping changes (that is, changes that would be flagged with in normal
			listing) differently. The overlapping lines in both files will be inserted by the edit script bracketed by and lines.

	      Produces a script that will incorporate only changes flagged
			, but treat these changes in the manner of option.

       The following command applies the resulting script to file1.

EXTERNAL INFLUENCES

   International Code Set Support
       Single- and multi-byte character code sets are supported.

WARNINGS

       Text lines that consist of a single period defeat

       Files longer than 64K bytes do not work.

FILES

SEE ALSO

       diff(1).

																	  diff3(1)