search

HelmholtzAI-Consultants-Munich / oligo-designer-toolsuite

Develop custom oligo design pipelines.
https://oligo-designer-toolsuite.readthedocs.io/en/latest/
13 stars 3 forks source link

Divide OligoAttributes into two classes #58

Open lisa-sousa opened 5 months ago

lisa-sousa commented 5 months ago

I would have two classes here: OligoAttributesCalculator (with the private functions) and OligoDatabaseAttributes which apply the functions to the database. The second one can have a common _apply_calculation(self, calc_function, **kwargs) function which iterates over the oligos and assigns attributes (with dynamic checks). The functions can also be static there

_Originally posted by @IsraMekki0 in https://github.com/HelmholtzAI-Consultants-Munich/oligo-designer-toolsuite/pull/51#discussion_r1555735735_

lisa-sousa commented 4 months ago

Additional improvement: parallelize the computation of oligo attributes for a database object.

lisa-sousa commented 2 months ago

Would be good to have a connection to the oligo database such that we don'z have to always instantiate the OligoAttributes class and then call it, e.g. maybe in the same way we get oligo attribute values, e.g. calculate_oligo_attributes(attribute_name, region_ids)? And then check if this oligo attribute can be computed. MAybe the same way as we do the sequence type checks?