The panel assessment function calculates the dimer load (both dimer count and mean deltaG) of an existing set of multiplex primers. The function runs Dimer Prediction, then Tabulates Dimers for deltaG=False (i.e., counts) and deltaG=True (i.e., mean deltaG), and prints out a summary.
import multiplex_wormhole as mw
mw.assessPanel(PRIMERS, ALL_DIMERS_dG=-8, END_DIMERS_dG=-4, BAD_DIMERS_dG=-10)
cd ~/multiplex_wormhole #navigate to where mw functions live
python3 panel_assessment.py -i INPUT [-a ALLDIMERS_DG] [-e ENDDIMERS_DG] [-b BADDIMERS_DG]
INPUT (-i) : Input primers, can be either CSV or FASTA format. If CSV, must have “PrimerID” and “Sequence” fields for conversion. ALL_DIMERS_dG (-a) : Gibbs free energy (delta G) threshold used to consider dimers not at 3’ ends. [Default: -8] END_DIMERS_dG (-e) : Gibbs free energy (delta G) threshold used to consider dimers at 3’ ends. [Default: -4] BAD_DIMERS_dG (-b) : Gibbs free energy (delta G) threshold used to consider dimers especially “bad”. [Default: -10]
All outputs take the basename of the input primer file.
PREFIX_MFEdimers.txtPREFIX_MFEdimers_ends.txtPREFIXPrimerPairDimers + sum.csv, wide.csv, binary_sum.csv, binary_wide.csvPREFIXPrimerPairDeltaG + mean.csv, wide.csvPrints out: