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DasLab / big_library_design

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Allow code to mutate away loop in barcode if it is causing problems #18

Open rkretsch opened 1 year ago

rkretsch commented 1 year ago

Currently, if desired barcode contains a stem-loop a fix sequence is used for the loop. Currently when the program has problems finding a barcode that matches the desired structure it will

  1. Reduce probability thresholds 3 times
  2. After those three times, if there is a polyA hang will allow this to mutate

So far these two steps have solved our problems, but if there is a case were the loop sequence is interacting heavily with the sequence of interest we could add

  1. After 2 more times, allow loop to mutate.
rkretsch commented 1 year ago

In fact some code already prepared and commented out for this purpose # new_loop = _get_random_barcode(num_bp=0, num5hang=len(loop),loop='').seq # uid = new_hang+uid[num5polyA:num5polyA+num_bp]+new_loop+uid[num5polyA+num_bp+len(loop):]