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Full Discussion: Subtracting values from 2 columns in a file
Top Forums UNIX for Dummies Questions & Answers Subtracting values from 2 columns in a file Post 302567475 by wolf_blue on Monday 24th of October 2011 09:49:38 AM
Old 10-24-2011
Subtracting values from 2 columns in a file
Hello,
I have a file with 5 columns that looks like this:

A1BG chr19 + 58863335 58866549
A1BG chr19 - 58858171 58864865
A2LD1 chr13 - 101182417 101186056
A2LD1 chr13 - 101182417 101241046
A2M chr12 - 9220303 9268558
A2ML1 chr12 + 8975149 9029377

I want to subtract the value in column 5 from column 4 and send the results to a 6th column and the file to look like this (6th col = values in 5th- values in 4thSmilie

A1BG chr19 + 58863335 58866549 3214
A1BG chr19 - 58858171 58864865 6694
A2LD1 chr13 - 101182417 101186056 3639
A2LD1 chr13 - 101182417 101241046 58629
A2M chr12 - 9220303 9268558 48255
A2ML1 chr12 + 8975149 9029377 54228


Then I want the file to get rid of the duplicates (I already used the sort and uniq commands and I still have some left e.g A1BG, A2LD1)
I want my final file to look like this, with only the genes with greatest length recorded (as below: only the largest values for genes A1BG and ALD1 were recorded:

A1BG chr19 - 58858171 58864865 6694
A2LD1 chr13 - 101182417 101241046 58629
A2M chr12 - 9220303 9268558 48255
A2ML1 chr12 + 8975149 9029377 54228

Please help!
Thanks so much!
 

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LEARN ABOUT NETBSD

comm

COMM(1) 						    BSD General Commands Manual 						   COMM(1)

NAME

     comm -- select or reject lines common to two files

SYNOPSIS

     comm [-123f] file1 file2

DESCRIPTION

     The comm utility reads file1 and file2, which should be sorted lexically, and produces three text columns as output: lines only in file1;
     lines only in file2; and lines in both files.

     The filename ``-'' means the standard input.

     The following options are available:

     -1      Suppress printing of column 1.

     -2      Suppress printing of column 2.

     -3      Suppress printing of column 3.

     -f      Fold case in line comparisons.

     Each column will have a number of tab characters prepended to it equal to the number of lower numbered columns that are being printed.  For
     example, if column number two is being suppressed, lines printed in column number one will not have any tabs preceding them, and lines
     printed in column number three will have one.

     comm assumes that the files are lexically sorted; all characters participate in line comparisons.

EXIT STATUS

     comm exits 0 on success, >0 if an error occurred.

SEE ALSO

     cmp(1), diff(1), sort(1), uniq(1)

STANDARDS

     The comm utility conforms to IEEE Std 1003.2-1992 (``POSIX.2'').

BSD
								   June 6, 1993 							       BSD
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