De-duplicate near redundant functions

[John-F-Wagstaff]

Is your feature request related to a problem? Please describe.
There are a number of near, but not quite redundant functions throughout the code, both due to development history and the re-contextualising effects of recent improvements to vv_hgvs.

Describe the solution you'd like
It would be good to keep track of these for later action, and some of these may now be removed, but care needs to be taken that the best is kept where possible.

Describe alternatives you've considered
Some near-redundant functions will be different enough in performance or action that keeping them separate is still useful, comments in the relevant function headers in these cases might be useful.

Additional context
Current list

• hgvs_to_delins_hgvs and hgvs_ref_alt
• multiple reverse compliment methods albeit with differing speed VS safety trade-offs e.g. bio-python, internal functions, etc

[Peter-J-Freeman]

The Biopython was removed in VV except for the API calls to RefSeq. These are not used much unless the database gets about a year or more out of date. Replaced with an internal fast rev comp function. I remembered you saying you wanted to remove this. I also think I have removed some revcomp functions too. And slimmed them down. There may be duplicates, though, agree here. We have at least 2 functions that string into del removed HGVS. Definitely worth investigating. Agree here.

[John-F-Wagstaff]

Ah that biopython call must have been removed in a later commit than the one I was reading, I think that there still is a couple of places where we have revcomp implementations in local functions for sections that where developed as separate modules first.

I hope it was OK anyway I needed to put it down to avoid forgetting, and I knew that the first function pair is still valid. If you can then feel free to add any function pairs to the list that look like possible candidates,

[Peter-J-Freeman]

Its a good plan and still relevant. There are definately duplicate functions.

def valstr(hgvs_variant):
    """
    format nucleotide descriptions to not display reference base and return a string
    """
    try:
        hgvs_variant.ac
    except AttributeError:
        raise AttributeError(f"valstr() called on {hgvs_variant} as a string. Must be a hgvs object")
    return str(remove_reference(hgvs_variant))

def remove_reference(hgvs_nucleotide):
    """
    format nucleotide descriptions to not display reference base, and return a string
    """
    hgvs_nucleotide_refless = hgvs_nucleotide.format({'max_ref_length': 0})
    return hgvs_nucleotide_refless

    def revcomp(self, bases):
        """
        Return the reverse complement of a nucleotide sequence.
        """
        return fn.simple_dna_revcomp(bases)

These are the ones I can remember.

Plus the stuff about the updated vvhgvs functionality will be a big win when it can be cleaned