CODEWITHSUNDEEP
sortingunix
user1631306
user1631306

Reputation: 4470

UNIX sort with -c

I have a file ( 3 columns tab delimited), I need to check if file is sorted or not Example:

chr1    9999999 10000125        C57T3ANXX:7:2114:14205:58915/2  50      -
chr1    10010918        10011044        C57T3ANXX:7:2310:08814:31632/1  50      +
chr1    10011185        10011311        C57T3ANXX:7:2310:08814:31632/2  50      -

On above file, I use 

cut -f1,2 f |sort -cn,

which give me 

sort: -:2: disorder: chr1       10010918.

I am not sure why, as the file is already sorted. I get same order when I use 

sort -k1,1 -k2,2 f

Upvotes: 1

Views: 405

Answers (1)

Zoltán Haindrich
Zoltán Haindrich

Reputation: 1808

sort -cn assumes that the entire line is the key, because the line starts with a non-numeric character it resorts to non-numeric mode for that key, which is the only one

enable numeric mode for you keys: sort -k1,1 -k2,2 -cn

Upvotes: 3

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