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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db2_field_precision

DB2_FIELD_PRECISION(3)							 1						    DB2_FIELD_PRECISION(3)

db2_field_precision - Returns the precision of the indicated column in a result set

SYNOPSIS

       int db2_field_precision (resource  $stmt, mixed	$column)

DESCRIPTION

	Returns the precision of the indicated column in a result set.

PARAMETERS

	      o $stmt
		- Specifies a statement resource containing a result set.

	      o $column
		-  Specifies  the  column in the result set. This can either be an integer representing the 0-indexed position of the column, or a
		string containing the name of the column.

RETURN VALUES

	Returns an integer containing the precision of the specified  column.  If  the	specified  column  does  not  exist  in  the  result  set,
       db2_field_precision(3) returns FALSE.

SEE ALSO

       db2_field_display_size(3), db2_field_name(3), db2_field_num(3), db2_field_scale(3), db2_field_type(3), db2_field_width(3).

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