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Top Forums Shell Programming and Scripting Join files on multiple fields Post 302950740 by sheetalk on Tuesday 28th of July 2015 10:37:38 AM
Old 07-28-2015
Join files on multiple fields

Hello all,

I want to join 2 tabbed files on the first 2 fields, and filling the missing values with 0. The 3rd column in each file is constant for the entire file.


file1
Code:
12658699	ST5	XX2720	0	1	0	1					
53039541	ST5	XX2720	1	0	1.5	1

file2
Code:
53039541	ST5	X23	0	1	0	1					
1267456	ST1	X23	1	0	1.4	1


Desired output
Code:
12658699	ST5	XX2720	0	1	0	1	X23	0	0	0	0
53039541	ST5	XX2720	1	0	1.5	1	X23	0	1	0	1
1267456	ST1	XX2720	0	0	0	0	X23	1	0	1.4	1

Its throwing me an error when I do the following, after sorting..

Code:
join  -a1 -a2  -t$'\t'   -1 1,2 -2 1,2 file1 file2
join: invalid field number: `1,2'

Please help !
 

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JOIN(1) 						      General Commands Manual							   JOIN(1)

NAME
join - relational database operator SYNOPSIS
join [ options ] file1 file2 DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If file1 is `-', the standard input is used. File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in each line. There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con- sists of the common field, then the rest of the line from file1, then the rest of the line from file2. Fields are normally separated by blank, tab or newline. In this case, multiple separators count as one, and leading separators are dis- carded. These options are recognized: -an In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2. -e s Replace empty output fields by string s. -jn m Join on the mth field of file n. If n is missing, use the mth field in each file. -o list Each output line comprises the fields specifed in list, each element of which has the form n.m, where n is a file number and m is a field number. -tc Use character c as a separator (tab character). Every appearance of c in a line is significant. SEE ALSO
sort(1), comm(1), awk(1) BUGS
With default field separation, the collating sequence is that of sort -b; with -t, the sequence is that of a plain sort. The conventions of join, sort, comm, uniq, look and awk(1) are wildly incongruous. JOIN(1)
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