Handle restriction enzymes with ambiguous sites

cerebis / qc3C

Reference-free quality assessment for Hi-C sequencing data

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Handle restriction enzymes with ambiguous sites #32

Closed cerebis closed 4 years ago

cerebis commented 5 years ago

At least the Arima library kit is documented to contain an enzyme recognising GANTC. Reverse lookup for site to enzyme name reports an example HinfI.

The current method qc3C.ligation.ligation_junction_seq() asserts no ambiguous sites, though this should be possible.

What is required is to validate matching conditions. Currently static string matching will need to be replaced by an alternative -- possibly regex.

cerebis commented 4 years ago

Resolved fully on cd93fc70b34ec478950c6a64471ddcd0de7c27b3