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Full Discussion: Join not working properly
Top Forums Shell Programming and Scripting Join not working properly Post 302879652 by RudiC on Friday 13th of December 2013 02:00:38 PM
Old 12-13-2013
Using your original files, I get this:
Code:
join -a1 -1 3 -2 1  file /tmp/mt4.genenames.txt
Medtr1g004990 XLOC_000005 XLOC_000005 chr1:35909-40554 q1 q2 OK 0.520378 6.91484 3.73206 6.85797 5e-05 0.000126299 yes down
Medtr1g006490 XLOC_000006 XLOC_000006 chr1:44429-46280 q1 q2 OK 16.1083 122.606 2.92814 10.2969 5e-05 0.000126299 yes down
join: /tmp/mt4.genenames.txt:6: is not sorted: Medtr1g004980    hypothetical protein
Medtr1g006600 XLOC_000008 XLOC_000008 chr1:51360-54977 q1 q2 OK 6.94505 3.84361 -0.853525 -2.49824 0.0001 0.000244358 yes up exostosin family protein
etc.

After sort /tmp/mt4.genenames.txt >/tmp/MED, I get
Code:
join -a1 -1 3 -2 1  file /tmp/MED 
Medtr1g004990 XLOC_000005 XLOC_000005 chr1:35909-40554 q1 q2 OK 0.520378 6.91484 3.73206 6.85797 5e-05 0.000126299 yes down casein kinase
Medtr1g006490 XLOC_000006 XLOC_000006 chr1:44429-46280 q1 q2 OK 16.1083 122.606 2.92814 10.2969 5e-05 0.000126299 yes down major intrinsic protein %28MIP%29 family transporter
Medtr1g006600 XLOC_000008 XLOC_000008 chr1:51360-54977 q1 q2 OK 6.94505 3.84361 -0.853525 -2.49824 0.0001 0.000244358 yes up exostosin family protein
Medtr1g006660 XLOC_000010 XLOC_000010 chr1:70777-71741 q1 q2 OK 1.15476 2.47771 1.10142 2.07776 0.0045 0.00841718 yes down AP2 domain class transcription factor
Medtr1g006975 XLOC_000014 XLOC_000014 chr1:129007-136403 q1 q2 OK 0.389401 0.166262 -1.2278 -2.00092 0.0017 0.00343409 yes up disease resistance protein %28CC-NBS-LRR class%29 family protein

, which is close to what you need, I believe.
This User Gave Thanks to RudiC For This Post:
 

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JOIN(1) 						    BSD General Commands Manual 						   JOIN(1)

NAME
join -- relational database operator SYNOPSIS
join [-a file_number | -v file_number] [-e string] [-o list] [-t char] [-1 field] [-2 field] file1 file2 DESCRIPTION
The join utility performs an ``equality join'' on the specified files and writes the result to the standard output. The ``join field'' is the field in each file by which the files are compared. The first field in each line is used by default. There is one line in the output for each pair of lines in file1 and file2 which have identical join fields. Each output line consists of the join field, the remaining fields from file1 and then the remaining fields from file2. The default field separators are tab and space characters. In this case, multiple tabs and spaces count as a single field separator, and leading tabs and spaces are ignored. The default output field separator is a single space character. Many of the options use file and field numbers. Both file numbers and field numbers are 1 based, i.e., the first file on the command line is file number 1 and the first field is field number 1. The following options are available: -a file_number In addition to the default output, produce a line for each unpairable line in file file_number. -e string Replace empty output fields with string. -o list The -o option specifies the fields that will be output from each file for each line with matching join fields. Each element of list has the either the form 'file_number.field', where file_number is a file number and field is a field number, or the form '0' (zero), representing the join field. The elements of list must be either comma (',') or whitespace separated. (The latter requires quoting to protect it from the shell, or, a simpler approach is to use multiple -o options.) -t char Use character char as a field delimiter for both input and output. Every occurrence of char in a line is significant. -v file_number Do not display the default output, but display a line for each unpairable line in file file_number. The options -v 1 and -v 2 may be specified at the same time. -1 field Join on the field'th field of file 1. -2 field Join on the field'th field of file 2. When the default field delimiter characters are used, the files to be joined should be ordered in the collating sequence of sort(1), using the -b option, on the fields on which they are to be joined, otherwise join may not report all field matches. When the field delimiter char- acters are specified by the -t option, the collating sequence should be the same as sort(1) without the -b option. If one of the arguments file1 or file2 is ``-'', the standard input is used. EXIT STATUS
The join utility exits 0 on success, and >0 if an error occurs. COMPATIBILITY
For compatibility with historic versions of join, the following options are available: -a In addition to the default output, produce a line for each unpairable line in both file 1 and file 2. -j1 field Join on the field'th field of file 1. -j2 field Join on the field'th field of file 2. -j field Join on the field'th field of both file 1 and file 2. -o list ... Historical implementations of join permitted multiple arguments to the -o option. These arguments were of the form 'file_number.field_number' as described for the current -o option. This has obvious difficulties in the presence of files named '1.2'. These options are available only so historic shell scripts do not require modification. They should not be used in new code. LEGACY DESCRIPTION
The -e option causes a specified string to be substituted into empty fields, even if they are in the middle of a line. In legacy mode, the substitution only takes place at the end of a line. Only documented options are allowed. In legacy mode, some obsolete options are re-written into current options. For more information about legacy mode, see compat(5). SEE ALSO
awk(1), comm(1), paste(1), sort(1), uniq(1), compat(5) STANDARDS
The join command conforms to IEEE Std 1003.1-2001 (``POSIX.1''). BSD
July 5, 2004 BSD
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