Usage of apply_cut in melt

[manulera]

Hi @BjornFJohansson,

I identified the reason why the tests fail after reverting to the previous form of apply_cut. Below a minimal example:

seq = Dseq("AGJGaGEg")

print(repr(seq))

# The problem is in this function:
ms1, ms2 = seq.get_ds_meltsites(2)

# Returns these values:
print(ms1)  # ((2, 2), None)
print(ms2)  # ((8, 1), None)

# Then it's followed with self.get_cutsite_pairs(), but
# the apply_cut that should be happening is this:
a = seq.apply_cut(None, ((2, 2), None))
b = seq.apply_cut(((3, 3), None), ((8, 2), None))  # Note how these are different
c = seq.apply_cut(((8, 1), None), None)

print()
print(repr(a))
print()
print(repr(b))
print()
print(repr(c))

Here is a representation, the X represents missing basepair

[manulera]

Just for documentation purposes, the new function relies on this behaviour where you can pass spaces to the watson and crick strands, and they will be ignored, and the overhang will be adjusted accordingly

from pydna.dseq import Dseq

seq = Dseq(b" GaGAg", b" CtCGCT", 2)

print(seq.ovhg)
print(repr(seq))

prints

3
Dseq(-8)
   GaGAg
TCGCtC