Separated minimums between design and simulate (#447)

* Separated minimums between design and simulate

* Added check on primer length when using simulate

* Added CHANGELOG.md

Author: whitead

CHANGELOG.md

@@ -5,6 +5,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Fixed
+ - Made it possible to simulate primers shorter than design minimum.
+
 ## [0.31.1] - 2024-01-31
 
 ### Added

primers/pcr/pcr.go

@@ -32,21 +32,24 @@ import (
 )
 
 // https://doi.org/10.1089/dna.1994.13.75
-var minimalPrimerLength int = 15
+const minimalPrimerLength int = 7
+
+// what we want for designs
+const designedMinimalPrimerLength int = 15
 
 // DesignPrimersWithOverhangs designs two primers to amplify a target sequence,
 // adding on an overhang to the forward and reverse strand. This overhang can
 // contain additional DNA needed for assembly, like Gibson assembly overhangs
 // or GoldenGate restriction enzyme sites.
 func DesignPrimersWithOverhangs(sequence, forwardOverhang, reverseOverhang string, targetTm float64) (string, string) {
 	sequence = strings.ToUpper(sequence)
-	forwardPrimer := sequence[0:minimalPrimerLength]
+	forwardPrimer := sequence[0:designedMinimalPrimerLength]
 	for additionalNucleotides := 0; primers.MeltingTemp(forwardPrimer) < targetTm; additionalNucleotides++ {
-		forwardPrimer = sequence[0 : minimalPrimerLength+additionalNucleotides]
+		forwardPrimer = sequence[0 : designedMinimalPrimerLength+additionalNucleotides]
 	}
-	reversePrimer := transform.ReverseComplement(sequence[len(sequence)-minimalPrimerLength:])
+	reversePrimer := transform.ReverseComplement(sequence[len(sequence)-designedMinimalPrimerLength:])
 	for additionalNucleotides := 0; primers.MeltingTemp(reversePrimer) < targetTm; additionalNucleotides++ {
-		reversePrimer = transform.ReverseComplement(sequence[len(sequence)-(minimalPrimerLength+additionalNucleotides):])
+		reversePrimer = transform.ReverseComplement(sequence[len(sequence)-(designedMinimalPrimerLength+additionalNucleotides):])
 	}
 
 	// Add overhangs to primer
@@ -168,6 +171,12 @@ func SimulateSimple(sequences []string, targetTm float64, circular bool, primerL
 // in your reaction, which can lead to confusing results. The variable
 // `circular` is for if the target template is circular, like a plasmid.
 func Simulate(sequences []string, targetTm float64, circular bool, primerList []string) ([]string, error) {
+	// make sure no primers are too short
+	for _, primer := range primerList {
+		if len(primer) < minimalPrimerLength {
+			return nil, errors.New("Primers are too short.")
+		}
+	}
 	initialAmplification := SimulateSimple(sequences, targetTm, circular, primerList)
 	subsequentAmplification := SimulateSimple(sequences, targetTm, circular, append(primerList, initialAmplification...))
 	if len(initialAmplification) != len(subsequentAmplification) {