Error if ~harmonize_rca used in GenBank

If the Genbank file has ~harmonize_rca(e_coli => h_sapiens), then running

from dnachisel import DnaOptimizationProblem
problem = DnaOptimizationProblem.from_record("example_sequence.gb")

returns

/path/to/DnaChisel/dnachisel/Specification/FeatureRepresentationMixin.py in from_label(cls, label, location, specifications_dict)
    127                 "Unknown parameter %s for specification %s "
    128                 "at location %s"
--> 129                 % (faulty_parameter, specification, kwargs["location"])
    130             )
    131 

TypeError: Unknown parameter e_coli  for specification harmonize_rca at location 1218-2308(+)

Same error for h_sapiens or h_sapiens_9606.

The function works with CodonOptimize(), e.g. CodonOptimize(species='h_sapiens', location=(0, 99), original_species='e_coli').

[Zulko]

CodonOptimize(species='h_sapiens', location=(0, 99), original_species='e_coli', method="harmonize_rca") returns HarmonizeRCA[0-99](h_sapiens) which is correct.

That’s not 100% correct, in an idea world it would return HarmonizeRCA[0-99](e_coli->h_sapiens). I think the feature->string conversion could be improved.

Indeed Snapgene Viewer saves a quoted annotation with 2x2 quote; for example /label=~harmonize_rca(““e_coli => h_sapiens””), so I recommend implementing this feature without quotes.

To be clear, the Genbank API should never use quotes, so you would use HarmonizeRCA("e_coli->h_sapiens") in a python script (equivalent to CodonOptimize(species='h_sapiens', original_species='e_coli', method="harmonize_rca")). But HarmonizeRCA(e_coli -> h_sapiens)` in a genbank file.

However, if I replace with -> in the code and use the attached example Genbank file, then it optimizes for E. coli:

Hmm that’s indeed a bug. ~harmonize_rca(e_coli -> h_sapiens) should set species to h_sapiens and origin_species to e_coli and it looks like it’s failing at that 🤔. I can probably help fix this over the weekend.

[Zulko]

Sorry for being unclear, I meant HarmonizeRCA("e_coli => h_sapiens") should work in a script. The genbank limitation is a bit annoying indeed. Some fields can have multiple lines, but not sure for labels.