Sort a tab delimited file based on column sort command bash

Question

I am trying to sort this file based on the fourth column. I want the file to reordered based on the values of the fourth column.

File:

2   1:103496792:A   0   103496792
3   1:103544434:A   0   103544434
4   1:103548497:A   0   103548497
1   1:10363487:T    0   10363487

I want it sorted like this:

1   1:10363487:T    0   10363487
2   1:103496792:A   0   103496792
3   1:103544434:A   0   103544434
4   1:103548497:A   0   103548497

I tried this command:

sort -t$'\t' -k1,1 -k2,2 -k3,3 -k 4,4 <filename>

But I get illegal variable name error. Can somebody help me with this?

score 47 · Accepted Answer · answered Jul 02 '13 at 16:12

47

To sort on the fourth column use just the -k 4,4 selector.

sort -t $'\t' -k 4,4 <filename>

You might also want -V which sorts numbers more naturally. For example, yielding 1 2 10 rather than 1 10 2 (lexicographic order).

sort -t $'\t' -k 4,4 -V <filename>

If you're getting errors about the $'\t' then make sure your shell is bash. Perhaps you're missing #!/bin/bash at the top of your script?

answered Jul 02 '13 at 16:12

John Kugelman

same error though.. illegal variable name. I dont know how to resolve it. I know the problem is with the $ – Vignesh Jul 02 '13 at 16:13
1

Make sure you are using bash and not `#!/bin/sh` or `sh script` – that other guy Jul 02 '13 at 16:16
2

Also, the `-t` option would be optional here, since the default column separator of "any whitespace" would suffice for your file. – chepner Jul 02 '13 at 17:30
Use "-n" to sort numerically. – Vladislavs Dovgalecs Jul 05 '17 at 23:05

score 4 · Answer 2 · answered Jul 02 '13 at 16:13

4

I believe you have an errant $ in your command.

Try:

sort -t\t -nk4

answered Jul 02 '13 at 16:13

Phylogenesis

2

`$'..'` is bash syntax for expanding escape sequences. In this case it expands to a literal tab. – that other guy Jul 02 '13 at 16:14
that helped but cant it order as 1 2 10 than 1 10 2 22?? – Vignesh Jul 02 '13 at 16:17
1

That's what the `-n` flag should be doing (numeric sort). – Phylogenesis Jul 02 '13 at 16:18

2 Answers2