Repository navigation
csvtk sort inconsistency #337
Description
Activity
- added a commit that references this issue
on Sep 28, 2025 You're right, it is a bug! Just fixed it.
I expect to tool to sort on all columns, if no column is specified.
Good suggestion!
It supports field ranges now, and the default value1-means all columns.Please have a try:
The help message is also updated with more details.
$ csvtk sort -h sort by selected fields Field types: - Column name : -k name - Nth field : -k 1 - field range: - All fields : -k 1- - From 3rd to 5th column : -k 3-5 - Fields except for the 4th : -k -4 - Fields except for 3rd-5th : -k -3--5 Sort types: - Default: alphabetical order : -k 1- - n : numeric order : -k 1:n - N : natrual order : -k 1:N (e.g., "a9" should be in front of "a10") - d : sort by date : -k 1:d (support multiple formats of date and time) - u : custom levels : -k 1:u -L levels.txt Combinations: - All sort types can be used with "r" for reversing the order, e.g., -k 1:nr - Multiple fields can be used, e.g., -k year:n -k name Usage: csvtk sort [flags] Flags: -h, --help help for sort -i, --ignore-case ignore-case -k, --keys strings keys (multiple values supported). sort type supported, "N" for natural order, "n" for number, "d" for date/time, "u" for user-defined order and "r" for reverse. e.g., "-k 1", "-k 2-", "-k 3-5:nr", "-k A:r", "-k 1:nr -k 2" (default [1-]) -L, --levels strings user-defined level file (one level per line, multiple values supported). format: <field>:<level-file>. e.g., "-k name:u -L name:level.txt"Thank you, it works perfectly now!
Also many thanks for the improved help text and the implementation of the field ranges, they are really helpful.
The only thing I noticed is the typo "natrual" in the help text, apart from that it looks great!Reacted by Wei ShenReacted by Wei Shenfixed and available in the new release.
Hi,
First of all, thanks for developing this tool! It's extremely useful in bioinformatics workflows.
I noticed an inconsistency in the
sortsubcommand.Example 1 (
test_1.tsv)Input:
Command:
Output:
Here, the rows are reordered because
+and-swapped positions.Example 2 (
test_2.csv)Input:
Command:
Output:
Again, the rows are reordered, but in the opposite way compared to the first example.
Problem
This is confusing because:
+and-.If I explicitly include the strand column in the sort keys, the output is as expected. However, my assumption was that if no columns are specified, the tool should sort using all columns. Why then does the behavior differ between these cases? Is there any situation where this inconsistency is intentional, or is it a bug?
I tested on version
0.31.0which is the most recent version available onbioconda.Thanks for looking into it!