Panel Assessment
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.
Usage
Command line syntax
mw-assess-panel -i INPUT [-a ALLDIMERS_DG] [-e ENDDIMERS_DG] [-b BADDIMERS_DG]
Python syntax
import multiplex_wormhole as mw
mw.assessPanel(PRIMERS, ALL_DIMERS_dG=-8, END_DIMERS_dG=-4, BAD_DIMERS_dG=-10)
Arguments
- 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]
Outputs
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.csv
Prints out:
- number of primer pairs
- total # pairwise dimers
- number of primer pairs involved in dimers
- dimers per pair
- mean deltaG of dimers
- Number of pairwise interactions with “bad” dimers
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