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moss-lab / ScanFold2.0

MIT License
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get_frag_feature_list() #3

Open EthanCC-1 opened 1 year ago

EthanCC-1 commented 1 year ago

This should probably be handled by a class. We should try to extend the Seq class from biopython so that we can just use the seq variable that's already there to get what we need, will greatly clean up the code and allow it to be expanded more easily

EthanCC-1 commented 1 year ago

either way we should create a "fragment" class that contains start/end coords, sequence, length, GC percent/ratio, AU ratio, mfe, structure, centroid, ed, and dinucleotide frequency

if we extend sequence we can give it a list of fragments that are found in that sequence, that would possibly let us handle multiple sequences in multiple threads simultaneously.

EthanCC-1 commented 1 year ago

the various "if algo ==" statements should be extracted to their own functions