Previously, a user could define a function in CATCH that implements a custom model to determine whether a probe hybridizes to a region of target sequence (e.g., to incorporate a calculation of free energy). The user would then need to set the cover_range_fn parameter where necessary (e.g., in the set_cover_filter module) to use this custom function.
This pull request makes it easier to use a custom function that determines hybridization. It exposes this ability by adding the --custom-hybridization-fn argument to the main design.py executable. (Likewise, it adds an argument for a more tolerant function to use with blacklisting genomes and differential identification.) The argument provides a path to a Python function, and CATCH dynamically loads this and uses it whenever it calculates hybridization between a probe and target sequence.
Coverage decreased (-0.2%) to 94.718% when pulling b8ef9f2db5f2c7b70e921f331ecc41427e1ed89a on custom-covg-fn into fe63b86bc41396c1da0b449ac440c6ae9e52b2c5 on master.
Previously, a user could define a function in CATCH that implements a custom model to determine whether a probe hybridizes to a region of target sequence (e.g., to incorporate a calculation of free energy). The user would then need to set the
cover_range_fn
parameter where necessary (e.g., in theset_cover_filter
module) to use this custom function.This pull request makes it easier to use a custom function that determines hybridization. It exposes this ability by adding the
--custom-hybridization-fn
argument to the maindesign.py
executable. (Likewise, it adds an argument for a more tolerant function to use with blacklisting genomes and differential identification.) The argument provides a path to a Python function, and CATCH dynamically loads this and uses it whenever it calculates hybridization between a probe and target sequence.