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Full Discussion: Join not working properly
Top Forums Shell Programming and Scripting Join not working properly Post 302879640 by ritakadm on Friday 13th of December 2013 12:58:09 PM
Old 12-13-2013
Join not working properly
I want to join two files , with file 1 col 3 and file 2 col 1 as key.
The join command is erratic for some reason. File 2 is a master file having all the names, and file 1 has some values. I want to add the names from fil2 in file 1. If I use the original master file, some output is missing.

For example Medtr1g004990 exists in the master file but does not come in the output.

However, if just use a truncated master file that has 5 records including Medtr1g004990, the output seems to be correct.

I have used sorted files also , same problem. Please help solve this, if join doesnt work,please let me know if some similar command to join would.

I have attached the original master file and pasted the truncated one.



File 1
Code:
# more Medtr1g006600.exp
XLOC_000005     XLOC_000005     Medtr1g004990   chr1:35909-40554        q1      q2      OK      0.520378        6.91484 3.73206 6.85797 5e-05   0.000126299     yes     down
XLOC_000006     XLOC_000006     Medtr1g006490   chr1:44429-46280        q1      q2      OK      16.1083 122.606 2.92814 10.2969 5e-05   0.000126299     yes     down
XLOC_000008     XLOC_000008     Medtr1g006600   chr1:51360-54977        q1      q2      OK      6.94505 3.84361 -0.853525       -2.49824        0.0001  0.000244358     yes     up
XLOC_000010     XLOC_000010     Medtr1g006660   chr1:70777-71741        q1      q2      OK      1.15476 2.47771 1.10142 2.07776 0.0045  0.00841718      yes     down
XLOC_000014     XLOC_000014     Medtr1g006975   chr1:129007-136403      q1      q2      OK      0.389401        0.166262        -1.2278 -2.00092        0.0017  0.00343409      yes     up

File 2 (truncated from attached file)
Code:
# more Medtr1g006600.annot
Medtr1g004990   casein kinase
Medtr1g006490   major intrinsic protein %28MIP%29 family transporter
Medtr1g006590   tonoplast intrinsic protein
Medtr1g006600   exostosin family protein
Medtr1g006605   hypothetical protein
Medtr1g006660   AP2 domain class transcription factor

Command and output with master file

Code:
 # join -a1 -1 3 -2 1  Medtr1g006600.exp 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
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

Command and output with truncated file

Code:
# join -a1 -1 3 -2 1  Medtr1g006600.exp Medtr1g006600.annot 
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

mt4.genenames.txt (2.27 MB) 
 

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