[Feature]: Double Runs

[sepandhaghighi]

Describe the feature you want to add

Double run length refers to how many times a dinucleotide base is repeated consecutively in a primer.

Describe your proposed solution

>>> from opr import Primer
>>> p1 = Primer("ATATCGAACACACACACA")
>>> p1.double_runs
{'GT': 0, 'CA': 5, 'AT': 2, 'TA': 0, 'GC': 0, 'GA': 0, 'AG': 0, 'TG': 0, 'CG': 0, 'TC': 0, 'AC': 5, 'CT': 0}

Describe alternatives you've considered, if relevant

No response

Additional context

References:

1. https://www.bioinformatics.org/sms2/pcr_primer_stats.html

[AHReccese]

TA is 0 or 1?
@sepandhaghighi
I'm trying to understand the concept, it is 0 since it has overlap with "AT", right?

[AHReccese]

I just see pass or warnings in the given link for the dinucleotide base.

[sepandhaghighi]

TA is 0 or 1? @sepandhaghighi I'm trying to understand the concept, it is 0 since it has overlap with "AT", right?

In consecutive mode, we begin with 2 instead of 1. However, this is merely a convention and not a rule. We can talk about it in our next weekly session.

[sepandhaghighi]

I just see pass or warnings in the given link for the dinucleotide base.

When a dinucleotide run length exceeds 5, this tool will alert you.

You can check it here:

https://www.bioinformatics.org/sms2/scripts/pcr_primer_stats.js