I am looking for something similar to the bash command comm, that I can use to select entries both unique to my 2 files and common to them. Comm worked great when I had just one column per file, eg.
comm -13 FILE1.txt FILE2.txt > Entries_only_in_file1.txt
But now I have multiple columns of info I wish to keep. I want to select column 2 as the one to filter rows for unique and common entries between my two files. If the entry in column two appears in both files I also want to record the info in columns 3,4,and 5 (if possible, this is not as important). Here is an example of input and output.
FILE1.txt
NM_023928 AACS 2 2 1
NM_182662 AADAT 2 2 1
NM_153698 AAED1 1 5 3
NM_001271 AAGAB 2 2 1
FILE2.txt
NM_153698 AAED1 2 5 3
NM_001271 AAGAB 2 2 1
NM_001605 AARS 3 40 37
NM_212533 ABCA2 3 4 2
Output wanted:
COMMON.txt
NM_153698 AAED1 1 5 3 2 5 3
NM_001271 AAGAB 2 2 1 2 2 1
UNIQUE_TO_1.txt
NM_023928 AACS 2 2 1
NM_182662 AADAT 2 2 1
UNIQUE_TO_2.txt
NM_001605 AARS 3 40 37
NM_212533 ABCA2 3 4 2
I know there has been similar questions before but I can't quite find what I'm looking for. Any ideas greatly appreciated, thank you.
join has the following options which are useful for your task:
-j FIELD: join on field FIELD-o FORMAT: specify output format, as a comma separated list of FILENUM.FIELD.-v FILENUM: output lines only on FILENUM.Common to both files:
$ join -j2 -o 1.1,1.2,1.3,1.4,1.5,2.3,2.4,2.5 FILE1.txt FILE2.txt
NM_153698 AAED1 1 5 3 2 5 3
NM_001271 AAGAB 2 2 1 2 2 1
Unique to FILE1:
$ join -j2 -v1 FILE1.txt FILE2.txt
AACS NM_023928 2 2 1
AADAT NM_182662 2 2 1
Unique to FILE2:
$ join -j2 -v2 FILE1.txt FILE2.txt
AARS NM_001605 3 40 37
ABCA2 NM_212533 3 4 2