CODEWITHSUNDEEP
sortingunix
PJx
PJx

Reputation: 1093

Unix sort: inconsistent between 2 files

[1.txt]
Sample10_1.fq.gz
Sample11_1.fq.gz
Sample12_1.fq.gz
Sample1_1.fq.gz
Sample13_1.fq.gz

[2.txt]
Sample10_2.fq.gz
Sample11_2.fq.gz
Sample12_2.fq.gz
Sample1_2.fq.gz
Sample13_2.fq.gz

As you can see, the only difference is the digit after the "_".

Anyway, here are the results of sort:

[sort 1.txt]
Sample10_2.fq.gz
Sample11_2.fq.gz
Sample12_2.fq.gz
Sample1_2.fq.gz
Sample13_2.fq.gz

[sort 2.txt]
Sample10_1.fq.gz
Sample11_1.fq.gz
Sample1_1.fq.gz
Sample12_1.fq.gz
Sample13_1.fq.gz

Discrepancy: "Sample1_" is sorted between "Sample12" and "Sample13" in 1.txt, but it's between "Sample11" and "Sample12" in 2.txt.

Am I doing something wrong to make this inconsistency happen?

Upvotes: 1

Views: 74

Answers (1)

U2EF1
U2EF1

Reputation: 13259

Use sort -V

cat 1.txt | sort -V
Sample1_1.fq.gz
Sample10_1.fq.gz
Sample11_1.fq.gz
Sample12_1.fq.gz
Sample13_1.fq.gz

Upvotes: 1

Related Questions