join not working

gamma_user · #1 (**permalink**) 05-07-2008

I was trying to merge the following two example files using their first field:

join -1 1 -2 1 file1 file 2

but nothing is produced. The expected result should be:

rs1005152 7 q21.3 3

It appears that the length of the first field in file1 is causing the problem. Any suggesting on how to use join to produce the desired result? I know there are other ways to get the result but I have to use the join because the real files are huge.

Thanks in advance.

file1:
rs10051507 5 q21.3
rs10051514 5 p15.32
rs10051527 5 q21.2
rs1005152 7 q21.3
rs10051540 5 q21.3
rs10051548 5 q21.1
rs1005155 X q27.3
rs10051594 5 q34

file2:
rs1003456 3
rs1005152 3

drl · #2 (**permalink**) 05-07-2008

Hi.

The files should be sorted on the join field:

Quote:

file1 and file2 must be sorted in increasing collating
sequence as determined by LC_COLLATE on the fields on which
they are to be joined, normally the first in each line (see
sort(1)).
--excerpt from Solaris man join, q.v.

Best wishes ... cheers, drl

gamma_user · #3 (**permalink**) 05-07-2008

Hi drl,

Both file1 and file2 have been sorted. Sorry for not making it clear. I also tried reverse sorting without success. Please help!

drl · #4 (**permalink**) 05-07-2008

Hi.

Here is a script that produces results for files not sorted, then sorted:

Code:

#!/usr/bin/env sh

# @(#) s1       Demonstrate join.

#  ____
# /
# |   Infrastructure BEGIN

echo
set -o nounset

debug=":"
debug="echo"

## The shebang using "env" line is designed for portability. For
#  higher security, use:
#
#  #!/bin/sh -

## Use local command version for the commands in this demonstration.

set +o nounset
LC_ALL=C ; LANG=C ; export LC_ALL LANG
echo "Environment: LC_ALL = $LC_ALL, LANG = $LANG"
echo "(Versions displayed with local utility \"version\")"
version >/dev/null 2>&1 && version =o $(_eat $0 $1) sort join
set -o nounset

echo

FILE1=data1
echo " Input file $FILE1:"
cat $FILE1

echo
FILE2=data2
echo " Input file $FILE2:"
cat $FILE2

echo
echo " Results expected:"
cat expected-results

# |   Infrastructure END
# \
#  ---

echo
echo " Results from processing without a sort:"
join $FILE1 $FILE2

echo
echo " Results from processing after sorting files:"
sort $FILE1 >t1
sort $FILE2 >t2
join t1 t2

exit 0

Yielding:

Code:

% ./s1

Environment: LC_ALL = C, LANG = C
(Versions displayed with local utility "version")
Linux 2.6.11-x1
GNU bash, version 2.05b.0(1)-release (i386-pc-linux-gnu)
sort (coreutils) 5.2.1
join (coreutils) 5.2.1

 Input file data1:
rs10051507 5 q21.3
rs10051514 5 p15.32
rs10051527 5 q21.2
rs1005152 7 q21.3
rs10051540 5 q21.3
rs10051548 5 q21.1
rs1005155 X q27.3
rs10051594 5 q34

 Input file data2:
rs1003456 3
rs1005152 3

 Results expected:
rs1005152 7 q21.3 3

 Results from processing without a sort:

 Results from processing after sorting files:
rs1005152 7 q21.3 3

cheers, drl

gamma_user · #5 (**permalink**) 05-08-2008

drl,

That's odd. I got the expected result when I ran your whole script. However when I ran each step of the script, join still did not work. Here is what I did:

$ cat data1
rs10051507 5 q21.3
rs10051514 5 p15.32
rs10051527 5 q21.2
rs1005152 7 q21.3
rs10051540 5 q21.3
rs10051548 5 q21.1
rs1005155 X q27.3
rs10051594 5 q34

$ cat data2
rs1003456 3
rs1005152 3

$ sort data1 >t1

$ sort data2>t2

$ join t1 t2

Why is that?

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