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Tuesday, September 17, 2013

Amazing GNU sort

I just came across this on Biostar: http://www.biostars.org/p/64687/

Question: How to sort bed format file
2
Is there any tools or commands to sort bed format file? The correct order is chr1, chr2, chr3, chr4,..., chr22, chrX, chrY.

3
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

1 comment:

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