Clearer error for I (inosine), or automatically treat it as N?

Attempting to call cutadapt v3.4 with a primer sequence containing “I” fails with:

Run "cutadapt --help" to see command-line options.
See https://cutadapt.readthedocs.io/ for full documentation.

cutadapt: error: Character 'I' in adapter sequence 'GYRGGGACGAAAGTCYYTGCI' is not a valid IUPAC code. Use only characters ABCDGHKMNRSTUVWXY

Inosine is found naturally at the wobble position of tRNA, and can match any base. Structurally similar to guanine (G), it preferentially binds cytosine ©. It sometimes used in primer design (Ben-Dov et al., 2006 https://doi.org/10.1128/aem.00849-06 ), where degeneracy N would give similar results.

In my own work I have mapped “I” to “N” when calling cutadapt with such a primer, and wondered if it would make sense to add .replace("I", "N") to cutadapt, or at least fail with a hint in this special case?, e.g.

Run "cutadapt --help" to see command-line options.
See https://cutadapt.readthedocs.io/ for full documentation.

cutadapt: error: Character 'I' in adapter sequence 'GYRGGGACGAAAGTCYYTGCI' is not a valid IUPAC code. For inosine consider using N instead.

[marcelm]

Ah, good find! So I guess that indeed means that at least one other person wants to use I for inosine.

[peterjc]

@TatyanaVl is the error message unclear?

Try using ‘CTCCTACGGGNGGCAGCAG’ with an ‘N’ instead of ‘CTCCTACGGGIGGCAGCAG’ with an ‘I’.