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Top Forums UNIX for Dummies Questions & Answers Merge two files with non-overlapping identities Post 302752829 by luoruicd on Monday 7th of January 2013 03:17:23 PM
Old 01-07-2013
Merge two files with non-overlapping identities

Hi All,
I wish to merge two files:
file1: with header
Code:
rsSNP-ID Chromosome Chr-Pos
rs171 1 175261679
rs242 1 20869461
rs538 1 6160958

file2: without header
Code:
disease:AAT deficiency:M0525101 rs1243168        20109307       1
disease:AAT deficiency:M0525101 rs4900229        20109307       1
disease:Abdominal Pain:PA446220 rs11209026       17068223       1
disease:Abdominal Pain:PA446220 rs11706052       20061166       1

I want to merge these two files with rsID (column 1 in file 1, column 2 in file 2) to create a file like this:
Code:
rs171 1 175261679  20109307       1 disease:AAT deficiency:M0525101
rs242 1 20869461  17068223       1 disease:Abdominal Pain:PA446220
rs538 1 6160958   17068223       1 disease:Abdominal Pain:PA446220

However, there are quite a lot of rsIDs, only in file 1, for those, I wish to create a line like this:
Code:
rsXXX 1 6160958   ""       0  ""

how can I do that?

Last edited by Scott; 01-07-2013 at 04:20 PM.. Reason: Code tags
 

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merge(1)																  merge(1)

NAME
merge - three-way file merge SYNOPSIS
merge [-Llabel1 [-Llabel3]] [-p] [-q] file1 file2 file3 DESCRIPTION
merge incorporates all changes that lead from file2 to file3 into file1. The result goes to standard output if -p is present, into file1 otherwise. merge is useful for combining separate changes to an original. Suppose file2 is the original, and both file1 and file3 are modifications of file2. Then merge combines both changes. An overlap occurs if both file1 and file3 have changes in a common segment of lines. On a few older hosts where diff3 does not support the -E option, merge does not detect overlaps, and merely supplies the changed lines from file3. On most hosts, if overlaps occur, merge out- puts a message (unless the -q option is given), and includes both alternatives in the result. The alternatives are delimited as follows: <<<<<<< file1 lines in file1 ======= lines in file3 >>>>>>> file3 If there are overlaps, the user should edit the result and delete one of the alternatives. If the -L label1 and -L label3 options are given, the labels are output in place of the names file1 and file3 in overlap reports. DIAGNOSTICS
Exit status is 0 for no overlaps, 1 for some overlaps, 2 for trouble. IDENTIFICATION
Author: Walter F. Tichy. Revision Number: 1.1.6.2; Release Date: 1993/10/07. Copyright (C) 1982, 1988, 1989 by Walter F. Tichy. Copyright (C) 1990, 1991 by Paul Eggert. SEE ALSO
diff3(1), diff(1), rcsmerge(1), co(1) merge(1)
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