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Top Forums Shell Programming and Scripting Finding out the common lines in two files using 4 fields with the help of awk and UNIX Post 302847473 by NamS on Tuesday 27th of August 2013 05:34:06 AM
Old 08-27-2013
Finding out the intersection in two files using 4 fields with the help of awk and UNIX

Dear All,
I have 2 files. If field 1, 2, 4 and 5 matches in both file1 and file2, I want to print the whole line of file1 and file2 one after another in my output file.

File1:
Code:
sc2/80         20      .        A       T         86       F=5;U=4
sc2/60         55      .        G       T         76       F=5;U=4 
sc2/68         20      .        T       C         71       F=5;U=4
sc2/24         24      .        T       G         31       F=5;U=4

File2:
Code:
sc2/99         84      .        C       G         61       F=5;U=4
sc2/80         20      .        A       T         30       F=5;U=4
sc2/60         40      .        G       T         76       F=5;U=4 
sc2/30         20      .        T       C         71       F=5;U=4
sc2/24         24      .        T       G         91       F=5;U=4

Expected Output:

Code:
sc2/80         20      .        A       T         86       F=5;U=4
sc2/80         20      .        A       T         30       F=5;U=4
sc2/24         24      .        T       G         31       F=5;U=4
sc2/24         24      .        T       G         91       F=5;U=4

I am new in the field and I appreciate your help.

Last edited by NamS; 08-27-2013 at 07:20 AM..
 

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DIFF(1) 						      General Commands Manual							   DIFF(1)

NAME
diff - differential file comparator SYNOPSIS
diff [ -efbh ] file1 file2 DESCRIPTION
Diff tells what lines must be changed in two files to bring them into agreement. If file1 (file2) is `-', the standard input is used. If file1 (file2) is a directory, then a file in that directory whose file-name is the same as the file-name of file2 (file1) is used. The normal output contains lines of these forms: n1 a n3,n4 n1,n2 d n3 n1,n2 c n3,n4 These lines resemble ed commands to convert file1 into file2. The numbers after the letters pertain to file2. In fact, by exchanging `a' for `d' and reading backward one may ascertain equally how to convert file2 into file1. As in ed, identical pairs where n1 = n2 or n3 = n4 are abbreviated as a single number. Following each of these lines come all the lines that are affected in the first file flagged by `<', then all the lines that are affected in the second file flagged by `>'. The -b option causes trailing blanks (spaces and tabs) to be ignored and other strings of blanks to compare equal. The -e option produces a script of a, c and d commands for the editor ed, which will recreate file2 from file1. The -f option produces a similar script, not useful with ed, in the opposite order. In connection with -e, the following shell program may help maintain multiple versions of a file. Only an ancestral file ($1) and a chain of version-to-version ed scripts ($2,$3,...) made by diff need be on hand. A `latest version' appears on the standard output. (shift; cat $*; echo '1,$p') | ed - $1 Except in rare circumstances, diff finds a smallest sufficient set of file differences. Option -h does a fast, half-hearted job. It works only when changed stretches are short and well separated, but does work on files of unlimited length. Options -e and -f are unavailable with -h. FILES
/tmp/d????? /usr/lib/diffh for -h SEE ALSO
cmp(1), comm(1), ed(1) DIAGNOSTICS
Exit status is 0 for no differences, 1 for some, 2 for trouble. BUGS
Editing scripts produced under the -e or -f option are naive about creating lines consisting of a single `.'. DIFF(1)
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