UNIX for Dummies Questions & Answers

Hi all

I´m a newbie so maybe this question will make someone mad.
I am trying this command;

Code:

join -a1 -11 file1 file2 > file3

file1 looks like:

Code:

1
2
3
4
5
6
7
8
9
10
11

file2:

Code:

1    lkj    klj    lkj
2    lkj    lkj    lkj
3
7    lkj    lkj    lkj
8
9
11    lkk    kll    lkk

The output skips the row numbered 11
While googeling I saw that join only understands alphabetic sorting but there must be a way to do this. My aim is to join five 60,000,000 lined files for a genetic project.

If my question is stupid maybe it´s because i´m not english speaking or that i´m a newbe in unix, please answer anyway, anything is appreciated.

Thanx in advance

Moderator's Comments:

Please use code tags <- click the link!

What OS are you using?

Update:
I can't replicate the problem you get when using join. I am not missing line 11 but getting a warning about the input files being not sorted, where this can be surpressed with an option in GNU join. The -1 1 can be left out as this seems to be default and you didn't define -2 1 anyway.

You can try this with awk:

Code:

$> awk 'NR==FNR{_[$1]=$0; next} _[$1] {print _[$1]; next} {print $0}' f2 f1
1    lkj    klj    lkj
2    lkj    lkj    lkj
3
4
5
6
7    lkj    lkj    lkj
8
9
10
11    lkk    kll    lkk

Is "Red Hat" a correct answer?

Now I´m confused, sometimes it works, sometimes not.
Now it complains that they are not sorted but still does the right thing.
The input files were originally created in the evil windows so that was maybe the problem.
It still is not trust worthy to get a warning when you want to trust the output file 100%

Thanx for the reply I´ll try the awk solution.

p.s. I was once nicknamed saxon

Heh, my name comes from an old arcade game though^^

"Red Hat" is ok - so we know it is Linux and you most probably use GNU versions of tools etc. There is incompatibility between some tools from different Linux'es and Unix'es.

It could be the case that ^M is causing a problem, if the file comes from windows. Could try the following to ensure a constant behaviour:

Code:

tr -d '\015' < f1 > f1.new
tr -d '\015' < f2 > f2.new
join -a1 f1.new f2.new

Yes the problem was some kind of linefeed issue

dos2unix does help

Saxon is a Rock group