Enhancement request: trim but keep adaptor, --action=trimupto

I have a usecase in mind were rather than adapter or primer sequence which I want to match and remove, I have markers for a region of interest, and I want the (possibly inexactly matched) marker to be retained in the output.

Currently there are four action modes (correct as of cutadapt v2.8):

$ cutadapt -h | grep "\-\-action" -A 4
  --action {trim,mask,lowercase,none}
                        What to do with found adapters. mask: replace with 'N'
                        characters; lowercase: convert to lowercase; none:
                        leave unchanged (useful with --discard-untrimmed).
                        Default: trim

Would you consider a new action mode, suggested name trimupto (trim up to) or trimuntil, as follows:

  --action {trim,mask,lowercase,trimupto,none}
                        What to do with found adapters. mask: replace with 'N'
                        characters; lowercase: convert to lowercase; trimupto:
                        trim up to but retaining the adapter; none: leave
                        unchanged (useful with --discard-untrimmed).
                        Default: trim

Left adapter example:

$ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -g AAAAAA -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done

Using --action trim:
>example
XXXXXXXXXXXGGGGGGRRRRRRR

Using --action mask:
>example
NNNNNNNNNNNNNNXXXXXXXXXXXGGGGGGRRRRRRR

Using --action lowercase:
>example
llllllllaaaaaaXXXXXXXXXXXGGGGGGRRRRRRR

Using --action none:
>example
LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR

Proposed output:

Using --action trimupto:
>example
AAAAAAXXXXXXXXXXXGGGGGGRRRRRRR

Using left and right adapter:

$ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -g AAAAAA...GGGGGG -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done

Using --action trim:
>example
XXXXXXXXXXX

Using --action mask:
>example
NNNNNNNNNNNNNNXXXXXXXXXXXNNNNNNNNNNNNN

Using --action lowercase:
>example
llllllllaaaaaaXXXXXXXXXXXggggggrrrrrrr

Using --action none:
>example
LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR

Proposed output:

Using --action trimupto:
>example
AAAAAAXXXXXXXXXXXGGGGGG

Right adapter example:

$ for ACTION in trim mask lowercase none; do echo; echo "Using --action $ACTION:"; cutadapt -a GGGGGG -o - example.fasta --quiet --discard-untrimmed --action $ACTION; done

Using --action trim:
>example
LLLLLLLLAAAAAAXXXXXXXXXXX

Using --action mask:
>example
LLLLLLLLAAAAAAXXXXXXXXXXXNNNNNNNNNNNNN

Using --action lowercase:
>example
LLLLLLLLAAAAAAXXXXXXXXXXXggggggrrrrrrr

Using --action none:
>example
LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGGRRRRRRR

Proposed output:

Using --action trimupto:
>example
LLLLLLLLAAAAAAXXXXXXXXXXXGGGGGG

[mariloubodde]

Thanks a lot! It looks like this should do exactly what I was hoping for; I will try it out tomorrow!

On 2020-12-03 13:45, Marcel Martin wrote:

I wanted to comment here, but the auto-close happened before I got around to it …

Yes, this is now implemented as --action=retain. I hope the behavior is as you both requested. I had suggested earlier that a special marker in the adapter specification would be a good way to do this, but I realized that implementing this as a different action actually is a lot easier, and not adding extra notation makes it easier for the users.

Documentation is at https://cutadapt.readthedocs.io/en/latest/guide.html#action .

@peterjc [1] The retain actually comes from you because you wrote

I want the […] marker to be retained in the output (emphasis mine). It’s a word I rarely use otherwise, so that makes it easy to search for in the documentation. I’ll release Cutadapt 3.1 with this feature included soon.

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[peterjc]

Lovely - I’m on leave right now, but hopefully I’ll get to try this out next month. Reading the documentation you’ve added, it should do what I was hoping for.