Closed Koeng101 closed 11 months ago
Sequence should be TTATAGGTCTCATACTAATAATTACACCGAGATAACACATCATGGATAAACCGATACTCAAAGATTCTATGAAGCTATTTGAGGCACTTGGTACGATCAAGTCGCGCTCAATGTTTGGTGGCTTCGGACTTTTCGCTGATGAAACGATGTTTGCACTGGTTGTGAATGATCAACTTCACATACGAGCAGACCAGCAAACTTCATCTAACTTCGAGAAGCAAGGGCTAAAACCGTACGTTTATAAAAAGCGTGGTTTTCCAGTCGTTACTAAGTACTACGCGATTTCCGACGACTTGTGGGAATCCAGTGAACGCTTGATAGAAGTAGCGAAGAAGTCGTTAGAACAAGCCAATTTGGAAAAAAAGCAACAGGCAAGTAGTAAGCCCGACAGGTTGAAAGACCTGCCTAACTTACGACTAGCGACTGAACGAATGCTTAAGAAAGCTGGTATAAAATCAGTTGAACAACTTGAAGAGAAAGGTGCATTGAATGCTTACAAAGCGATACGTGACTCTCACTCCGCAAAAGTAAGTATTGAGCTACTCTGGGCTTTAGAAGGAGCGATAAACGGCACGCACTGGAGCGTCGTTCCTCAATCTCGCAGAGAAGAGCTGGAAAATGCGCTTTCTTAAATGAAGAGACCATATA
@Koeng101 was this ever resolved?
No. I fixed it in bioscript but not here. I'll port the fix when I get the chance.
What's the status of this? @Koeng101 need help with it?
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)
Will take a crack at this as a break from #297 /administrative stuff.
Great! This is very important.
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
}
Output:
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.