Unclear what warning message "g/--remove-gaps to remove spaces" means

[SHuang-Broad]

Prerequisites

• make sure you're are using the latest version by seqkit version
• read the usage

Describe your issue

describe the problem

Warning message when running the following command

$ seqkit seq -m 10000 <path_to_fastq.gz> | gzip > <output.fastq.gz>

�[33m[WARN]�[0m you may switch on flag -g/--remove-gaps to remove spaces

The usage page documents -g as removing gaps as opposed to removing spaces (which looks more likely to be right).
Assuming that it is indeed "removing gaps", does it mean that bases that are literally N will be dropped?

Second, what could be triggering this warning message? I'd hope my FASTQ doesn't have spaces in its sequence lines....

provide a reproducible example

Unfortunately, the data I work with is protected. Sorry about this.

Thank you!
Steve

[shenwei356]

Hi Steve, it's triggered by options -m or -M for filtering squence by lenght, just in case there are some spaces in the sequences which might result in incorrect outputs.

By default, -g removes "- \t." which can be set by :

-G, --gap-letters string        gap letters (default "- \t.")

You're right, it's more like removing spaces not gaps in most scenarios. I used the “gap” in case of multiple sequence alignment files, where the gap is marked as “-”.

[SHuang-Broad]

Thanks for the explanation!
It looks like you've labeled this a todo item, so I'll leave this open. (But please feel free to close it when appropriate).

[shenwei356]

Updated

  -g, --remove-gaps               remove gaps letters set by -G/--gap-letters, e.g., spaces, tabs, and
                                  dashes (gaps "-" in aligned sequences)
  -G, --gap-letters string        gap letters to be removed with -g/--remove-gaps (default "- \t.")