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Tuesday, September 17, 2013

Amazing GNU sort

I just came across this on Biostar:

Question: How to sort bed format file
Is there any tools or commands to sort bed format file? The correct order is chr1, chr2, chr3, chr4,..., chr22, chrX, chrY.

GNU sort can now sort in alpha-numeric order. See option "-V, --version-sort" of the following version "sort (GNU coreutils) 8.17".
Here is an example:
$ echo -e "chr10\t1\t2\tA\nchr2\t1\t2\tB\nchr1\t1\t2\tC"
chr10   1       2       A
chr2    1       2       B
chr1    1       2       C
And the result is:
$ echo -e "chr10\t1\t2\tA\nchr2\t1\t2\tB\nchr1\t1\t2\tC" | sort -k1,1V
chr1    1       2       C
chr2    1       2       B
chr10   1       2       A

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