This adds functionality to design, at the same time, primers that bound an amplicon and guides between those primers. The amplicon length can be variable (not a fixed window length, in contrast to previous usage). Primer design is done in the primer_search module and combined primer+guide design is done in the target_search module. The combined search operates according to a specified cost function, and finds and outputs the best N targets based on cost.
There are now two commands in design_guides.py: guides-from-sliding-window and complete-targets. The first does what design_guides.py had previously done: output guides within each window of a fixed width. The second provides the new functionality, outputting both primers and guides.
This adds functionality to design, at the same time, primers that bound an amplicon and guides between those primers. The amplicon length can be variable (not a fixed window length, in contrast to previous usage). Primer design is done in the
primer_searchmodule and combined primer+guide design is done in thetarget_searchmodule. The combined search operates according to a specified cost function, and finds and outputs the best N targets based on cost.There are now two commands in
design_guides.py:guides-from-sliding-windowandcomplete-targets. The first does whatdesign_guides.pyhad previously done: output guides within each window of a fixed width. The second provides the new functionality, outputting both primers and guides.