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@github-actions github-actions released this 04 Dec 16:45
· 118 commits to main since this release
v0.17.7
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Release notes

new method Design.base_pairs()

This method returns a dict mapping helix idx's where base pairs exist to a list of offsets where those base pairs are.

Domain/Extension/Loopout colors

Individual Domain's, Extension's, and Loopout's now have a color field. If specified, then this overrides the field Strand.color when displayed in the web interface. There is also a new method StrandBuilder.with_domain_color():

helices = [sc.Helix(max_offset=100) for _ in range(4)]
design = sc.Design(helices=helices, grid=sc.square)

red = sc.Color(255, 0, 0)
dark_red = sc.Color(150, 0, 0)
green = sc.Color(0, 255, 0)
dark_green = sc.Color(0, 150, 0)
blue = sc.Color(0, 0, 255)
dark_blue = sc.Color(0, 0, 150)
black = sc.Color(0, 0, 0)

design.draw_strand(0, 0) \
    .extension_5p(num_bases=5).with_domain_color(red) \
    .move(8).with_domain_color(green) \
    .loopout(1, 5).with_domain_color(dark_blue) \
    .move(-8).with_domain_color(dark_red) \
    .cross(2) \
    .move(8).with_domain_color(dark_green) \
    .cross(3) \
    .move(-8) \
    .extension_3p(num_bases=5).with_domain_color(black) \
    .with_color(blue)

image

Commits

  • 5586c9f: bumped version (David Doty) #256
  • 6463865: closes #252: add method Design.base_pairs() (David Doty) #254
  • fec6f43: changed return type of Design.base_pairs() to dict and added allow_mismatches parameter (David Doty) #254
  • e795627: fixed unit tests after updating with_sequence and with_domain_sequence to default to not assigning complement (David Doty) #254
  • 6b6001a: removed unused _popleft() function (David Doty) #254
  • e55609d: Update scadnano.py (David Doty) #256
  • afc44b8: don't put Helix idx in base_pairs dict if Helix has no base pairs (David Doty) #256
  • 1049cdc: fixed base pair calculation to allow for deletions/insertions/wildcards/None if DNA sequence is not assigned (David Doty) #256
  • e6c0737: added unit test for no base pairs (David Doty) #256
  • f81b8ff: Update scadnano_tests.py (David Doty) #256
  • 7b83a43: fixed bug in Design.base_pairs() when no reverse domains on helix (David Doty) #256
  • 5312a59: Update scadnano_tests.py (David Doty) #256
  • 1b7e605: closes #238: Domain colors (David Doty) #255
  • fea3b32: added example with domain colors (David Doty) #256
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