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Add ApplyMethylation to mark methyltransferase sites - #116
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* Add ApplyMethylation to mark methyltransferase sites ApplyMethylation lowercases the bases each methyltransferase would methylate, producing a sequence that can be fed into CutWithEnzyme / GoldenGate with methylated=true so a methylation-blocked Type IIS site fails to cut in simulation, reproducing the in-vitro block. Circular parts are scanned doubled (mirroring CutWithEnzyme) so a site spanning the origin is still marked, and marks from the second copy are folded back onto the returned single-copy sequence. Adds TestApplyMethylation covering a linear site, a circular site at the origin, and a circular site that spans the origin. * Use real Dcm methyltransferase in TestApplyMethylation The earlier test used a made-up methyltransferase recognizing the BsaI site, which marked the wrong bases. Dcm (CCWGG) is the real host methylation that blocks GoldenGate cuts, and it marks CcAgG. Rewrite the three cases around Dcm on the CCAGG site formed by the test sequences. --------- Ported from #113, which merged into fragment-with-break (go/lib layout) rather than main. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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ApplyMethylation lowercases the bases each methyltransferase would
methylate, producing a sequence that can be fed into CutWithEnzyme /
GoldenGate with methylated=true so a methylation-blocked Type IIS site
fails to cut in simulation, reproducing the in-vitro block.
Circular parts are scanned doubled (mirroring CutWithEnzyme) so a site
spanning the origin is still marked, and marks from the second copy are
folded back onto the returned single-copy sequence.
Adds TestApplyMethylation covering a linear site, a circular site at the
origin, and a circular site that spans the origin.
The earlier test used a made-up methyltransferase recognizing the BsaI
site, which marked the wrong bases. Dcm (CCWGG) is the real host
methylation that blocks GoldenGate cuts, and it marks CcAgG. Rewrite the
three cases around Dcm on the CCAGG site formed by the test sequences.
Ported from #113, which merged into fragment-with-break (go/lib layout)
rather than main.
Co-Authored-By: Claude Opus 5.5 noreply@anthropic.com