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Edinburgh-Genome-Foundry / GoldenHinges

:link: Short overhangs design for DNA assembly
https://edinburgh-genome-foundry.github.io/GoldenHinges/
MIT License
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Decomposing circular sequences #4

Open veghp opened 3 years ago

veghp commented 3 years ago
  1. Cut similar-length fragments: the two end fragments in a circular sequence are actually joined and thus the fragment doesn't have the desired length.
  2. Cut in featured zones: the issue doesn't apply here. However, this option can be used as a workaround for the above, by specifying !cut regions at regular intervals on the circle.

A simple solution is to add an option to cut_sequence() that adjusts the cut points for circular sequences: https://github.com/Edinburgh-Genome-Foundry/GoldenHinges/blob/b4af31d671189956c55a3339a2946861a64e5f02/goldenhinges/OverhangsSelector.py#L382

A full solution could consider any rotation of the sequence. However, this does not seem to be practically necessary.

Suggestions are welcome.