PCR simulations are wrong.

[Koeng101]

package main

import (
	"fmt"
	"github.com/TimothyStiles/poly/primers/pcr"
)

func main() {
	gene := "aataattacaccgagataacacatcatggataaaccgatactcaaagattctatgaagctatttgaggcacttggtacgatcaagtcgcgctcaatgtttggtggcttcggacttttcgctgatgaaacgatgtttgcactggttgtgaatgatcaacttcacatacgagcagaccagcaaacttcatctaacttcgagaagcaagggctaaaaccgtacgtttataaaaagcgtggttttccagtcgttactaagtactacgcgatttccgacgacttgtgggaatccagtgaacgcttgatagaagtagcgaagaagtcgttagaacaagccaatttggaaaaaaagcaacaggcaagtagtaagcccgacaggttgaaagacctgcctaacttacgactagcgactgaacgaatgcttaagaaagctggtataaaatcagttgaacaacttgaagagaaaggtgcattgaatgcttacaaagcgatacgtgactctcactccgcaaaagtaagtattgagctactctgggctttagaaggagcgataaacggcacgcactggagcgtcgttcctcaatctcgcagagaagagctggaaaatgcgctttcttaa"

	fragments, _ := pcr.Simulate([]string{gene}, 55.0, false, []string{"TATATGGTCTCTTCATTTAAGAAAGCGCATTTTCCAGC", "TTATAGGTCTCATACTAATAATTACACCGAGATAACACATCATGG", "CTGCAGGTCGACTCTAG"})

	// Now let's make sure it only amplified our target.
	fmt.Println(fragments[0])

}

Output:

TATATGGTCTCTTCATTTACACCGAGATAACACATCATGGATAAACCGATACTCAAAGATTCTATGAAGCTATTTGAGGCACTTGGTACGATCAAGTCGCGCTCAATGTTTGGTGGCTTCGGACTTTTCGCTGATGAAACGATGTTTGCACTGGTTGTGAATGATCAACTTCACATACGAGCAGACCAGCAAACTTCATCTAACTTCGAGAAGCAAGGGCTAAAACCGTACGTTTATAAAAAGCGTGGTTTTCCAGTCGTTACTAAGTACTACGCGATTTCCGACGACTTGTGGGAATCCAGTGAACGCTTGATAGAAGTAGCGAAGAAGTCGTTAGAACAAGCCAATTTGGAAAAAAAGCAACAGGCAAGTAGTAAGCCCGACAGGTTGAAAGACCTGCCTAACTTACGACTAGCGACTGAACGAATGCTTAAGAAAGCTGGTATAAAATCAGTTGAACAACTTGAAGAGAAAGGTGCATTGAATGCTTACAAAGCGATACGTGACTCTCACTCCGCAAAAGTAAGTATTGAGCTACTCTGGGCTTTAGAAGGAGCGATAAACGGCACGCACTGGAGCGTCGTTCCTCAATCTCGCAGAGAAGAGCTGGAAAATGCGCTTTCTTAAATGAAGAGACCATATA

Check here - https://pkg.go.dev/github.com/TimothyStiles/poly@v0.21.1/primers/pcr

TTATAGGTCTCATACTAATAATTACACCGAGATAACACATCATGG anneals to the beginning of the sequence, NOT TATATGGTCTCTTCATTTAAGAAAGCGCATTTTCCAGC. There is no reason why the beginning of the output sequence should be TATA

@TimothyStiles This is a fairly critical bug we should figure out.

[Koeng101]

Sequence should be TTATAGGTCTCATACTAATAATTACACCGAGATAACACATCATGGATAAACCGATACTCAAAGATTCTATGAAGCTATTTGAGGCACTTGGTACGATCAAGTCGCGCTCAATGTTTGGTGGCTTCGGACTTTTCGCTGATGAAACGATGTTTGCACTGGTTGTGAATGATCAACTTCACATACGAGCAGACCAGCAAACTTCATCTAACTTCGAGAAGCAAGGGCTAAAACCGTACGTTTATAAAAAGCGTGGTTTTCCAGTCGTTACTAAGTACTACGCGATTTCCGACGACTTGTGGGAATCCAGTGAACGCTTGATAGAAGTAGCGAAGAAGTCGTTAGAACAAGCCAATTTGGAAAAAAAGCAACAGGCAAGTAGTAAGCCCGACAGGTTGAAAGACCTGCCTAACTTACGACTAGCGACTGAACGAATGCTTAAGAAAGCTGGTATAAAATCAGTTGAACAACTTGAAGAGAAAGGTGCATTGAATGCTTACAAAGCGATACGTGACTCTCACTCCGCAAAAGTAAGTATTGAGCTACTCTGGGCTTTAGAAGGAGCGATAAACGGCACGCACTGGAGCGTCGTTCCTCAATCTCGCAGAGAAGAGCTGGAAAATGCGCTTTCTTAAATGAAGAGACCATATA

[TimothyStiles]

@Koeng101 was this ever resolved?

[Koeng101]

No. I fixed it in bioscript but not here. I'll port the fix when I get the chance.

[carreter]

What's the status of this? @Koeng101 need help with it?

[Koeng101]

Yes, this is actually pretty high priority as well, and I should have fixed it earlier (and haven't used this part of poly since I haven't fixed it yet)

[carreter]

Will take a crack at this as a break from #297 /administrative stuff.

[Koeng101]

Great! This is very important.

[carreter]

Sneaky little bug...

func generatePcrFragments(sequence string, forwardLocation int, reverseLocation int, forwardPrimerIndxs []int, reversePrimerIndxs []int, minimalPrimers []string, primerList []string) []string {
	var pcrFragments []string
	for forwardPrimerIndex := range forwardPrimerIndxs { // We were iterating over indexes of forwardPrimerIndxs rather than the values themselves, which is what we actually want!
		minimalPrimer := minimalPrimers[forwardPrimerIndex]
		fullPrimerForward := primerList[forwardPrimerIndex]
		for _, reversePrimerIndex := range reversePrimerIndxs {
			fullPrimerReverse := transform.ReverseComplement(primerList[reversePrimerIndex])
			pcrFragment := fullPrimerForward[:len(fullPrimerForward)-len(minimalPrimer)] + sequence[forwardLocation:reverseLocation] + fullPrimerReverse
			pcrFragments = append(pcrFragments, pcrFragment)
		}
	}
	return pcrFragments
}