dual barcoding improvements (#67)

This adds "name" field to dual barcodes, as well as a way to create dual barcode primer sets from a list of dual barcodes, rather than just from a csv file.

README.md

@@ -71,6 +71,7 @@ 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]
+- Updated dual barcodes primer sets to be created without csv files [#67](https://github.com/Koeng101/dnadesign/pull/67)
 - Added workers to bio as a way to process data [#62](https://github.com/Koeng101/dnadesign/pull/62)
 - Improved megamash efficiency and added []Match JSON conversion [#61](https://github.com/Koeng101/dnadesign/pull/61)
 - Added barcoding functionality for sequencing reads [#59](https://github.com/Koeng101/dnadesign/pull/59)

lib/sequencing/barcoding/barcoding.go

@@ -173,10 +173,48 @@ type DualBarcodePrimerSet struct {
 
 // DualBarcode contains a forward and reverse barcode.
 type DualBarcode struct {
+	Name    string
 	Forward string
 	Reverse string
 }
 
+// DualBarcodesToPrimerSet parsers a list of dual barcodes into a dual barcode
+// primer set.
+func DualBarcodesToPrimerSet(dualBarcodes []DualBarcode) DualBarcodePrimerSet {
+	var result DualBarcodePrimerSet
+	result.BarcodeMap = make(map[string]DualBarcode)
+	result.ReverseBarcodeMap = make(map[DualBarcode]string)
+	forwardBarcodesMap := make(map[string]bool)
+	reverseBarcodesMap := make(map[string]bool)
+
+	for _, barcode := range dualBarcodes {
+		forwardBarcodesMap[barcode.Forward] = true
+		reverseBarcodesMap[barcode.Reverse] = true
+		newDualBarcode := DualBarcode{Forward: barcode.Forward, Reverse: barcode.Reverse}
+		result.BarcodeMap[barcode.Name] = newDualBarcode
+		result.ReverseBarcodeMap[newDualBarcode] = barcode.Name
+	}
+	// Convert maps to slices
+	forwardBarcodes := make([]string, 0, len(forwardBarcodesMap))
+	for barcode := range forwardBarcodesMap {
+		forwardBarcodes = append(forwardBarcodes, barcode)
+	}
+	reverseBarcodes := make([]string, 0, len(reverseBarcodesMap))
+	for barcode := range reverseBarcodesMap {
+		reverseBarcodes = append(reverseBarcodes, barcode)
+	}
+
+	// Sort the slices
+	sort.Strings(forwardBarcodes)
+	sort.Strings(reverseBarcodes)
+
+	// Append sorted barcodes to result
+	result.ForwardBarcodes = forwardBarcodes
+	result.ReverseBarcodes = reverseBarcodes
+
+	return result
+}
+
 // ParseDualPrimerSet parses a csv file into a DualBarcodePrimerSet.
 func ParseDualPrimerSet(csvFile io.Reader) (DualBarcodePrimerSet, error) {
 	var result DualBarcodePrimerSet

lib/sequencing/barcoding/barcoding_test.go

@@ -1,11 +1,13 @@
-package barcoding
+package barcoding_test
 
 import (
 	_ "embed"
 	"fmt"
 	"strings"
+	"testing"
 
 	"github.com/koeng101/dnadesign/lib/bio"
+	"github.com/koeng101/dnadesign/lib/sequencing/barcoding"
 	"github.com/koeng101/dnadesign/lib/sequencing/nanopore"
 )
 
@@ -32,15 +34,15 @@ ATGTTGCCTACCTACTTGGTTCAGTTACGTATTGCTAAGGTTAACACAAAGACACCCGACAACTTTCTTCAGCACCTGCC
 +
 %%%%%%####$%(*+,)&''));::80-''')0000BCFJOSNLQJKJKRSMSFKLSDHIMGJEHDABFCCHIJKSSISHGJMSKSSKSOLSJSJIOJMSMNRKJKSJQLISGHGIHSJHSLJKSMISJEEBBCBH>=:/---849000>@GEEEJOKJIJHGSISIOMHKKGFGFJMGHHROIPSIJSSJKSLSMMSKJSJIIIKNMMEISKMLSKSHJPHLMJNQLHGRJKKKSHKKOMISOSGFJIOSSLSOSSSSNMSIFH876'&'(....+++(%`
 
-	primerSet, _ := ParseSinglePrimerSet(strings.NewReader(primerSetCsv))
+	primerSet, _ := barcoding.ParseSinglePrimerSet(strings.NewReader(primerSetCsv))
 	parser := bio.NewFastqParser(strings.NewReader(reads))
 	records, _ := parser.Parse()
 
 	var barcodes []string
 	for _, record := range records {
 		// Note: Nanopore has a score that requires a lower match (~16) than the
 		// default ScoreMagicNumber (18).
-		barcode, _ := SingleBarcodeSequence(record.Sequence, primerSet)
+		barcode, _ := barcoding.SingleBarcodeSequence(record.Sequence, primerSet)
 		if barcode != "" {
 			barcodes = append(barcodes, barcode)
 		}
@@ -102,13 +104,13 @@ GTGTGTACTTCGTTCAGTTACGTATGCTTAGTTGTGAACACAAAGACACCGACAACTTCTTCAGCACCTTCTTGATCTTC
 +
 $$$%%%%&',*+,//;=:9771111,-+*&&%%%%%'.1389:987777844443553((50+,,88:;2///;6555597677764334578879999:977778888888;=;99888766534424551666688767644445776777:<;:998986652222378*9:::<;:99876322211//..,,,,-0667873333488('''122../
 `
-	primerSet, _ := ParseDualPrimerSet(strings.NewReader(primerSetCsv))
+	primerSet, _ := barcoding.ParseDualPrimerSet(strings.NewReader(primerSetCsv))
 	parser := bio.NewFastqParser(strings.NewReader(reads))
 	records, _ := parser.Parse()
 
 	var wells []string
 	for _, record := range records[0:10] {
-		well, _ := DualBarcodeSequence(record.Sequence, primerSet)
+		well, _ := barcoding.DualBarcodeSequence(record.Sequence, primerSet)
 		if well != "" {
 			wells = append(wells, well)
 		}
@@ -117,3 +119,11 @@ $$$%%%%&',*+,//;=:9771111,-+*&&%%%%%'.1389:987777844443553((50+,,88:;2///;655559
 	fmt.Println(wells)
 	// Output: [B15 O1 O1 J22 C22 E20 A15]
 }
+
+func TestDualBarcodesToPrimerSet(t *testing.T) {
+	dualBarcodes := []barcoding.DualBarcode{{Name: "test", Forward: "ATG", Reverse: "TAA"}}
+	primerSet := barcoding.DualBarcodesToPrimerSet(dualBarcodes)
+	if len(primerSet.ForwardBarcodes) != 1 || len(primerSet.ReverseBarcodes) != 1 {
+		t.Errorf("Should have gotten barcode length of 1.")
+	}
+}