Question

I’m trying to sort a string of letters and numbers alphanumerically in an “intuitive”/natural way using the unix sort command, but cannot get it to sort properly. I have this file:

$ cat ~/headers 
@42EBKAAXX090828:6:100:1699:328/2
@42EBKAAXX090828:6:10:1077:1883/2
@42EBKAAXX090828:6:102:785:808/2

I’d like to sort it alphanumerically, where intuitively @42EBKAAXX090828:6:10:... is first (since 10 is smaller than 100 and 102), second is @42EBKAAXX090828:6:100... and third is @42EBKAAXX090828:6:102:204:1871/2.

I know that suggest sorting on a particular position within the line, but the position of the : here could vary and so this would not be a general and workable solution here.

I tried:

sort --stable -k1,1 ~/headers > foo

with various combinations of -n and -u parameters but it does not give the correct ordering.

How can this be done efficiently, either from bash using sort or from Python? I’d like to apply this to files that are round 4-5 GB in size, so containing millions of lines.

Thanks!

Answer 1

the -V option appears to do what you want – natural sorting. Intended for version numbers apparently (hence the letter chosen)

sort -V ~/headers

outputs

@42EBKAAXX090828:6:10:1077:1883/2
@42EBKAAXX090828:6:100:1699:328/2
@42EBKAAXX090828:6:102:785:808/2