X-Git-Url: https://git.arvados.org/lightning.git/blobdiff_plain/83983adc7d02cb2b460eede7341313d54379c8c3..00b2acd54dd1aa412f6f2bddc24b1bbb31c7ae3f:/exportnumpy.go?ds=sidebyside

diff --git a/exportnumpy.go b/exportnumpy.go
index d67ac6fee7..ec6c83b886 100644
--- a/exportnumpy.go
+++ b/exportnumpy.go
@@ -1,4 +1,4 @@
-package main
+package lightning
 
 import (
 	"bufio"
@@ -11,10 +11,13 @@ import (
 	"net/http"
 	_ "net/http/pprof"
 	"os"
+	"path"
 	"sort"
+	"strings"
 
 	"git.arvados.org/arvados.git/sdk/go/arvados"
 	"github.com/kshedden/gonpy"
+	"github.com/sirupsen/logrus"
 	log "github.com/sirupsen/logrus"
 )
 
@@ -37,8 +40,9 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 	priority := flags.Int("priority", 500, "container request priority")
 	inputFilename := flags.String("i", "-", "input `file`")
 	outputFilename := flags.String("o", "-", "output `file`")
-	annotationsFilename := flags.String("output-annotations", "", "output `file` for tile variant annotations tsv")
-	librefsFilename := flags.String("output-onehot2tilevar", "", "when using -one-hot, create tsv `file` mapping column# to tag# and variant#")
+	annotationsFilename := flags.String("output-annotations", "", "output `file` for tile variant annotations csv")
+	librefsFilename := flags.String("output-onehot2tilevar", "", "when using -one-hot, create csv `file` mapping column# to tag# and variant#")
+	labelsFilename := flags.String("output-labels", "", "output `file` for genome labels csv")
 	onehot := flags.Bool("one-hot", false, "recode tile variants as one-hot")
 	cmd.filter.Flags(flags)
 	err = flags.Parse(args)
@@ -64,9 +68,11 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 			Name:        "lightning export-numpy",
 			Client:      arvados.NewClientFromEnv(),
 			ProjectUUID: *projectUUID,
-			RAM:         128000000000,
+			RAM:         450000000000,
 			VCPUs:       32,
 			Priority:    *priority,
+			KeepCache:   1,
+			APIAccess:   true,
 		}
 		err = runner.TranslatePaths(inputFilename)
 		if err != nil {
@@ -76,8 +82,9 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 			fmt.Sprintf("-one-hot=%v", *onehot),
 			"-i", *inputFilename,
 			"-o", "/mnt/output/matrix.npy",
-			"-output-annotations", "/mnt/output/annotations.tsv",
-			"-output-onehot2tilevar", "/mnt/output/onehot2tilevar.tsv",
+			"-output-annotations", "/mnt/output/annotations.csv",
+			"-output-onehot2tilevar", "/mnt/output/onehot2tilevar.csv",
+			"-output-labels", "/mnt/output/labels.csv",
 			"-max-variants", fmt.Sprintf("%d", cmd.filter.MaxVariants),
 			"-min-coverage", fmt.Sprintf("%f", cmd.filter.MinCoverage),
 			"-max-tag", fmt.Sprintf("%d", cmd.filter.MaxTag),
@@ -95,18 +102,19 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 	if *inputFilename == "-" {
 		input = ioutil.NopCloser(stdin)
 	} else {
-		input, err = os.Open(*inputFilename)
+		input, err = open(*inputFilename)
 		if err != nil {
 			return 1
 		}
 		defer input.Close()
 	}
+	input = ioutil.NopCloser(bufio.NewReaderSize(input, 8*1024*1024))
 	tilelib := &tileLibrary{
 		retainNoCalls:       true,
 		retainTileSequences: true,
 		compactGenomes:      map[string][]tileVariantID{},
 	}
-	err = tilelib.LoadGob(context.Background(), input, nil)
+	err = tilelib.LoadGob(context.Background(), input, strings.HasSuffix(*inputFilename, ".gz"), nil)
 	if err != nil {
 		return 1
 	}
@@ -139,7 +147,32 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 	}
 
 	log.Info("building numpy array")
-	out, rows, cols := cgs2array(tilelib.compactGenomes)
+	out, rows, cols, names := cgs2array(tilelib)
+
+	if *labelsFilename != "" {
+		log.Infof("writing labels to %s", *labelsFilename)
+		var f *os.File
+		f, err = os.OpenFile(*labelsFilename, os.O_CREATE|os.O_WRONLY, 0777)
+		if err != nil {
+			return 1
+		}
+		defer f.Close()
+		_, outBasename := path.Split(*outputFilename)
+		for i, name := range names {
+			_, err = fmt.Fprintf(f, "%d,%q,%q\n", i, trimFilenameForLabel(name), outBasename)
+			if err != nil {
+				err = fmt.Errorf("write %s: %w", *labelsFilename, err)
+				return 1
+			}
+		}
+		err = f.Close()
+		if err != nil {
+			err = fmt.Errorf("close %s: %w", *labelsFilename, err)
+			return 1
+		}
+	}
+
+	log.Info("writing numpy file")
 	var output io.WriteCloser
 	if *outputFilename == "-" {
 		output = nopCloser{stdout}
@@ -167,9 +200,12 @@ func (cmd *exportNumpy) RunCommand(prog string, args []string, stdin io.Reader,
 			}
 		}
 	}
-	log.Info("writing numpy")
+	log.WithFields(logrus.Fields{
+		"rows": rows,
+		"cols": cols,
+	}).Info("writing numpy")
 	npw.Shape = []int{rows, cols}
-	npw.WriteUint16(out)
+	npw.WriteInt16(out)
 	err = bufw.Flush()
 	if err != nil {
 		return 1
@@ -188,7 +224,7 @@ func (*exportNumpy) writeLibRefs(fnm string, tilelib *tileLibrary, librefs []til
 	}
 	defer f.Close()
 	for i, libref := range librefs {
-		_, err = fmt.Fprintf(f, "%d\t%d\t%d\n", i, libref.Tag, libref.Variant)
+		_, err = fmt.Fprintf(f, "%d,%d,%d\n", i, libref.Tag, libref.Variant)
 		if err != nil {
 			return err
 		}
@@ -196,31 +232,53 @@ func (*exportNumpy) writeLibRefs(fnm string, tilelib *tileLibrary, librefs []til
 	return f.Close()
 }
 
-func cgs2array(cgs map[string][]tileVariantID) (data []uint16, rows, cols int) {
-	var cgnames []string
-	for name := range cgs {
+func cgs2array(tilelib *tileLibrary) (data []int16, rows, cols int, cgnames []string) {
+	for name := range tilelib.compactGenomes {
 		cgnames = append(cgnames, name)
 	}
-	sort.Strings(cgnames)
+	sort.Slice(cgnames, func(i, j int) bool {
+		return trimFilenameForLabel(cgnames[i]) < trimFilenameForLabel(cgnames[j])
+	})
 
-	rows = len(cgs)
-	for _, cg := range cgs {
+	rows = len(tilelib.compactGenomes)
+	for _, cg := range tilelib.compactGenomes {
 		if cols < len(cg) {
 			cols = len(cg)
 		}
 	}
-	data = make([]uint16, rows*cols)
+
+	// flag low-quality tile variants so we can change to -1 below
+	lowqual := make([]map[tileVariantID]bool, cols/2)
+	for tag, variants := range tilelib.variant {
+		lq := lowqual[tag]
+		for varidx, hash := range variants {
+			if len(tilelib.seq[hash]) == 0 {
+				if lq == nil {
+					lq = map[tileVariantID]bool{}
+					lowqual[tag] = lq
+				}
+				lq[tileVariantID(varidx+1)] = true
+			}
+		}
+	}
+
+	data = make([]int16, rows*cols)
 	for row, name := range cgnames {
-		for i, v := range cgs[name] {
-			data[row*cols+i] = uint16(v)
+		for i, v := range tilelib.compactGenomes[name] {
+			if v > 0 && lowqual[i/2][v] {
+				data[row*cols+i] = -1
+			} else {
+				data[row*cols+i] = int16(v)
+			}
 		}
 	}
+
 	return
 }
 
-func recodeOnehot(in []uint16, incols int) (out []uint16, librefs []tileLibRef, outcols int) {
+func recodeOnehot(in []int16, incols int) (out []int16, librefs []tileLibRef, outcols int) {
 	rows := len(in) / incols
-	maxvalue := make([]uint16, incols)
+	maxvalue := make([]int16, incols)
 	for row := 0; row < rows; row++ {
 		for col := 0; col < incols; col++ {
 			if v := in[row*incols+col]; maxvalue[col] < v {
@@ -242,7 +300,7 @@ func recodeOnehot(in []uint16, incols int) (out []uint16, librefs []tileLibRef,
 	}
 	log.Printf("recodeOnehot: dropped %d input cols with zero maxvalue", dropped)
 
-	out = make([]uint16, rows*outcols)
+	out = make([]int16, rows*outcols)
 	for inidx, row := 0, 0; row < rows; row++ {
 		outrow := out[row*outcols:]
 		for col := 0; col < incols; col++ {
@@ -260,3 +318,17 @@ type nopCloser struct {
 }
 
 func (nopCloser) Close() error { return nil }
+
+func trimFilenameForLabel(s string) string {
+	if i := strings.LastIndex(s, "/"); i >= 0 {
+		s = s[i+1:]
+	}
+	s = strings.TrimSuffix(s, ".gz")
+	s = strings.TrimSuffix(s, ".fa")
+	s = strings.TrimSuffix(s, ".fasta")
+	s = strings.TrimSuffix(s, ".1")
+	s = strings.TrimSuffix(s, ".2")
+	s = strings.TrimSuffix(s, ".gz")
+	s = strings.TrimSuffix(s, ".vcf")
+	return s
+}