Gnu join - join two files by specified field
目录
- Gnu join - join two files by specified field
- Basic usage
- The very useful options for GNU join
- -a1 - print unmatched lines in file1;
- -a2 - print unmatched lines in file2
- -a1 -a2 - print unmatched lines in both file1 and file2
- -o - To align the output in table format, use the option to custome the output
- -t - To use the TAB as output delimiter
- –check-order - join requires the input file sorted, if join with 1st column, please sort the input files using 1st columns before use join. And to make sure there is no problem, use this option to check.
- -e - To make the output format more strict and use this option to fill missing columns. This helps greatly if you need to process the file in the downstreaming analysis.
Basic usage
Create two files with TAB delimiter
file1:
a 1
b 1
d 1
e 1
g 1
file2:
a 2
b 2
c 2
e 2
f 2
Join them use join:
join -1 1 -2 1 file1 file2
Output:
a 1 2
d 1 2
e 1 2
The very useful options for GNU join
-a1 - print unmatched lines in file1;
join -1 1 -1 1 file1 file2 -a1
Output:
a 1 2
b 1
d 1 2
e 1 2
g 1
-a2 - print unmatched lines in file2
join -1 1 -1 1 file1 file2 -a2
Output:
a 1 2
c 2
d 1 2
e 1 2
f 2
-a1 -a2 - print unmatched lines in both file1 and file2
join -1 1 -1 1 file1 file2 -a1 -a2
Output:
a 1 2
b 1
c 2
d 1 2
e 1 2
f 2
g 1
Be careful that tab is not aligned well.
-o - To align the output in table format, use the option to custome the output
join -1 1 -1 1 file1 file2 -a1 -a2 -o 0,1.2,2.2
0 means the joined column.
1.2 means print the column 2 in file1;
2.2 means print the column 2 in file2;
Output:
a 1 2
b 1
c 2
d 1 2
e 1 2
f 2
g 1
If file1 and files have more than 2 columns, modify the -o string
-t - To use the TAB as output delimiter
join -1 1 -1 1 file1 file2 -a1 -a2 -o 0,1.2,2.2 -t$'\t'
Output:
a 1 2
b 1
c 2
d 1 2
e 1 2
f 2
g 1
–check-order - join requires the input file sorted, if join with 1st column, please sort the input files using 1st columns before use join. And to make sure there is no problem, use this option to check.
join -1 1 -1 1 file1 file2 -a1 -a2 -o 0,1.2,2.2 -t$'\t' --check-order
Output:
a 1 2
b 1
c 2
d 1 2
e 1 2
f 2
g 1
Create non-sorted file3:
a 3
d 3
c 3
e 3
f 3
join file1 and file3:
join -1 1 -1 1 file1 file3 -a1 -a2 -o 0,1.2,2.2 -t$'\t' --check-order
Output with error message:
a 1 3
b 1
join: file3:3: is not sorted: c 3
-e - To make the output format more strict and use this option to fill missing columns. This helps greatly if you need to process the file in the downstreaming analysis.
join -1 1 -1 1 file1 file2 -a1 -a2 -o 0,1.2,2.2 -t$'\t' --check-order -eNULL
Output:
a 1 2
b 1 NULL
c NULL 2
d 1 2
e 1 2
f NULL 2
g 1 NULL
Output is a very tidy table.
