working version

this is working….4 million reads in 2.5 mins on a 2012 macbook

cmd/sblade/main.go

@@ -1,7 +1,7 @@
 package main
 
 import (
-	"fmt"
+	//"fmt"
 	bio "github.com/crmackay/gobioinfo"
 	"github.com/crmackay/switchblade/workers"
 	"runtime"
@@ -11,7 +11,7 @@ import (
 /*
 func work (input chan FASTARead, ouput chan FASTARead) {
     //processRead.Process
-    fmt.Println("Starting Worker:")
+    //fmt.Println("Starting Worker:")
 }*/
 
 func main() {
@@ -25,13 +25,15 @@ func main() {
 	runtime.GOMAXPROCS(totalCPUS)
 
 	CPUWorkers := totalCPUS - 1
-	CPUWorkers = 1
+	// CPUWorkers = 1
 	//rawReads := make(chan bio.FASTQRead, 1000)
 
 	//processedReads := make(chan bio.FASTQRead, 1000)
 
 	// TODO set path to input file
-	inFile := "/Users/christophermackay/Desktop/deepseq_data/pir1/hits-clip/working_data/sample_data/fastq/sblade-test/sample_25000_2.fastq"
+	// inFile := "/Users/christophermackay/Desktop/deepseq_data/pir1/hits-clip/working_data/sample_data/fastq/sblade-test/sample_10.fastq"
+
+	inFile := "/Users/christophermackay/Desktop/deepseq_data/pir1/hits-clip/working_data/sample_data/fastq/sblade-test/2014_06_HITS_CLIP_1_2_3_4+PhiX_NoIndex_L003_R1_001.fastq.gz"
 
 	outFile := "/Users/christophermackay/Desktop/deepseq_data/pir1/hits-clip/working_data/sample_data/fastq/sblade-test/output.fastq"
 	// TODO set path to output file
@@ -57,17 +59,17 @@ func main() {
 
 	// wait until the are all done
 	numDones := 0
+	//fmt.Println("numCPUWorkers", CPUWorkers)
 	for numDones < CPUWorkers {
 		<-doneSignal
 		numDones++
 		wg.Done()
-		fmt.Println("Number of Dones: ", numDones)
+		//fmt.Println("Number of Dones: ", numDones)
 	}
 	close(finishedReads)
 	close(outputData)
-	<-doneSignal
 	wg.Done()
 	wg.Wait()
 
-	fmt.Println("this is the main function")
+	//fmt.Println("this is the main function")
 }

cmd/test-crosscompile/main.go

@@ -0,0 +1,18 @@
+package main
+
+import (
+	"fmt"
+	"runtime"
+)
+
+func main() {
+	// find the number of logical CPUs on the system
+	totalCPUS := runtime.NumCPU()
+
+	fmt.Println("total CPUs", totalCPUS)
+	// set the golang runtime to use all the available processors
+	runtime.GOMAXPROCS(totalCPUS)
+
+	CPUWorkers := totalCPUS - 1
+	fmt.Println("CPU workers", CPUWorkers)
+}

fiveprime/barcodes.go

@@ -1,7 +1,7 @@
 package fiveprime
 
 import (
-	"fmt"
+	// "fmt"
 	bio "github.com/crmackay/gobioinfo"
 	config "github.com/crmackay/switchblade/config"
 	sw "github.com/crmackay/switchblade/types"
@@ -195,7 +195,7 @@ func inferBarcode(b string, q []uint8) string {
 	seqProbs := make(map[string]float64)
 
 	for k := range config.Barcodes {
-		fmt.Println(k)
+		// fmt.Println(k)
 		probSeq := float64(1)
 		bcode := []rune(k)
 		for i, elem := range b {
@@ -207,7 +207,7 @@ func inferBarcode(b string, q []uint8) string {
 			}
 
 		}
-		fmt.Println(probSeq)
+		// fmt.Println(probSeq)
 		seqProbs[k] = probSeq
 	}
 
@@ -217,15 +217,15 @@ func inferBarcode(b string, q []uint8) string {
 		denominator += v * config.BarcodeRatios[k]
 
 	}
-	fmt.Println("denominator: ", denominator)
+	// fmt.Println("denominator: ", denominator)
 	bcProbs := make(map[string]float64)
 	for k, v := range seqProbs {
 		// TODO change this to the correct ration (0.2 and 0.3)
 		probBarcodeGivenSeq := (v * config.BarcodeRatios[k]) / denominator
 		bcProbs[k] = probBarcodeGivenSeq
 
 	}
-	fmt.Println(bcProbs)
+	// fmt.Println(bcProbs)
 
 	trueBarcode := maxProbBarcode(bcProbs)
 
@@ -248,7 +248,7 @@ func maxProbBarcode(m map[string]float64) string {
 		}
 		i++
 	}
-	fmt.Println(maxK, maxV)
+	// fmt.Println(maxK, maxV)
 	return maxK
 
 }

threeprime/prob.go

@@ -18,7 +18,7 @@ determine whether the sequence in question is a contaminant or not.
 package threeprime
 
 import (
-	"fmt"
+	//"fmt"
 	bio "github.com/crmackay/gobioinfo"
 	//sw "github.com/crmackay/switchblade"
 	"github.com/crmackay/switchblade/config"
@@ -119,12 +119,12 @@ func threePLinkerTest(a bio.PairWiseAlignment, r bio.FASTQRead, testNum int) boo
 
 	queryPosition := testStart
 
-	fmt.Println(a.ExpandedCIGAR)
+	// fmt.Println(a.ExpandedCIGAR)
 	for _, elem := range a.ExpandedCIGAR {
 		// track position along query string, especially to keep track of indels
 
-		//fmt.Println(queryPosition, string(elem))
-		fmt.Println(queryPosition, string(elem))
+		// fmt.Println(queryPosition, string(elem))
+		// fmt.Println(queryPosition, string(elem))
 		switch {
 		case string(elem) == "m":
 			probSeqGivenContam *= probContamGivenMatch(r.PHRED.Decoded[queryPosition])
@@ -155,7 +155,6 @@ func threePLinkerTest(a bio.PairWiseAlignment, r bio.FASTQRead, testNum int) boo
 			// in the case of a calculated deletion in the query seqeuence, we
 			// do not increment queryPosition, since we are effectively in a
 			// "gap" in the query string
-			fmt.Println("hello")
 
 		case string(elem) == "j":
 			probSeqGivenContam *= probContamGivenIndel()
@@ -195,10 +194,10 @@ func threePLinkerTest(a bio.PairWiseAlignment, r bio.FASTQRead, testNum int) boo
 		((probSeqGivenContam * probContam) + (probSeqGivenChance * (1 - probContam)))
 
 		// fmt.Printf("probChanceGivenSeq: %20.400f", probChanceGivenSeq)
-	fmt.Println("probChanceGivenSeq", probChanceGivenSeq)
+	// fmt.Println("probChanceGivenSeq", probChanceGivenSeq)
 	// fmt.Printf("probContamGivenSeq: %20.400f", probContamGivenSeq)
-	fmt.Println("probContamGivenSeq", probContamGivenSeq)
-	fmt.Println()
+	// fmt.Println("probContamGivenSeq", probContamGivenSeq)
+	// fmt.Println()
 	// test P(L|S) > P(C|S)
 
 	if probContamGivenSeq > probChanceGivenSeq {

threeprime/trim.go

@@ -2,7 +2,7 @@ package threeprime
 
 import (
 	//"errors"
-	"fmt"
+	//"fmt"
 	//bio "github.com/crmackay/gobioinfo"
 	sw "github.com/crmackay/switchblade/types"
 	//data "github.com/crmackay/switchblade/research"
@@ -59,19 +59,17 @@ func Process3p(r *sw.Read) {
 
 	still3pContam := true
 
-	pos3p := len(r.Sequence) - 1
-	fmt.Println(pos3p)
-	fmt.Println(len(config.Linker5p))
+	// fmt.Println(pos3p)
+	// fmt.Println(len(config.Linker5p))
 	for still3pContam {
 		// if len(config.Linker5p) < pos3p {
 		// 	still3pContam, pos3p = next3pAlign(r)
 		// 	fmt.Println(string(r.Sequence))
 		// 	fmt.Println(still3pContam, pos3p)
 		// }
-
-		still3pContam, pos3p = next3pAlign(r)
-		fmt.Println(string(r.Sequence))
-		fmt.Println(still3pContam, pos3p)
+		still3pContam, _ = next3pAlign(r)
+		// fmt.Println(string(r.Sequence))
+		// fmt.Println(still3pContam, pos3p)
 	}
 
 	trim3p(r)

workers/workers.go

@@ -2,7 +2,7 @@ package workers
 
 import (
 	"encoding/csv"
-	"fmt"
+	//"fmt"
 	bio "github.com/crmackay/gobioinfo"
 	"github.com/crmackay/switchblade/fiveprime"
 	"github.com/crmackay/switchblade/research"
@@ -18,7 +18,7 @@ import (
 // and puts some meta data about the trimming work that was completed in a
 //tab-deliminted format into a
 func Trimmer(rawReads chan *bio.FASTQRead, finishedReads chan<- *bio.FASTQRead, outputData chan<- []string, doneChan chan bool) {
-	fmt.Println("starting worker")
+	//fmt.Println("starting worker")
 	for rawRead := range rawReads {
 
 		inProcessRead := types.NewRead(rawRead)
@@ -29,9 +29,9 @@ func Trimmer(rawReads chan *bio.FASTQRead, finishedReads chan<- *bio.FASTQRead,
 
 		data := research.GetDataCSV(inProcessRead)
 
-		fmt.Println(inProcessRead.DNASequence.Sequence)
-		fmt.Println(inProcessRead.End5p)
-		fmt.Println(inProcessRead.End3p)
+		//fmt.Println(inProcessRead.DNASequence.Sequence)
+		//fmt.Println(inProcessRead.End5p)
+		//fmt.Println(inProcessRead.End3p)
 		var finishedRead *bio.FASTQRead
 		if inProcessRead.End5p < inProcessRead.End3p {
 			finishedRead = &bio.FASTQRead{
@@ -47,7 +47,7 @@ func Trimmer(rawReads chan *bio.FASTQRead, finishedReads chan<- *bio.FASTQRead,
 				Misc: inProcessRead.Barcode + ":" + inProcessRead.DegenBases,
 			}
 		} else {
-			fmt.Println(string(inProcessRead.DNASequence.Sequence))
+			//fmt.Println(string(inProcessRead.DNASequence.Sequence))
 			finishedRead = &bio.FASTQRead{
 				DNASequence: bio.DNASequence{
 					Sequence: inProcessRead.DNASequence.Sequence[inProcessRead.End5p:inProcessRead.End5p],
@@ -68,7 +68,7 @@ func Trimmer(rawReads chan *bio.FASTQRead, finishedReads chan<- *bio.FASTQRead,
 
 	}
 	doneChan <- true
-	fmt.Println("Sending Done")
+	//fmt.Println("Sending Done")
 	return
 }
 
@@ -86,7 +86,7 @@ func ReadWriter(inFile string, outFile string, rawReads chan *bio.FASTQRead, fin
 
 	csvfile, err := os.Create(dataPath + ".csv")
 	if err != nil {
-		fmt.Println("Error:", err)
+		//fmt.Println("Error:", err)
 		return
 	}
 	defer csvfile.Close()
@@ -125,12 +125,10 @@ func ReadWriter(inFile string, outFile string, rawReads chan *bio.FASTQRead, fin
 
 	for read := range finishedReads {
 		doneWriter.Write(*read)
-
-	}
-	for data := range outputData {
+		data := <-outputData
 		dataWriter.WriteAll([][]string{data})
 
 	}
-	doneSignal <- true
+
 	return
 }