Plot import stats.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>

diff --git a/cmd.go b/cmd.go
index 2e59e51b76358da62fd519f9e554232cb888560b..18e18f0d4a16c034c8aca21fced9dd3d7fc2d04e 100644 (file)
--- a/cmd.go
+++ b/cmd.go
@@ -21,6 +21,7 @@ var (
                "ref2genome":         &ref2genome{},
                "vcf2fasta":          &vcf2fasta{},
                "import":             &importer{},
+               "import-stats-plot":  &importstatsplot{},
                "export":             &exporter{},
                "export-numpy":       &exportNumpy{},
                "filter":             &filterer{},

diff --git a/go.mod b/go.mod
index e880e3788d3d33c7c12fde978c28115bdc477bc5..890032ac3975313536c2be733468d32304ca8fff 100644 (file)
--- a/go.mod
+++ b/go.mod
@@ -22,6 +22,7 @@ require (
        golang.org/x/net v0.0.0-20200520182314-0ba52f642ac2
        golang.org/x/sys v0.0.0-20200519105757-fe76b779f299 // indirect
        gonum.org/v1/gonum v0.8.1
+       gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b
        gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15
        gopkg.in/yaml.v2 v2.3.0 // indirect
 )

diff --git a/go.sum b/go.sum
index 973623f01d146061ca566fba83102b17fa619a11..c390d8ce57f259c0359b45e82fbb9bff27566ad6 100644 (file)
--- a/go.sum
+++ b/go.sum
@@ -8,6 +8,7 @@ github.com/Azure/azure-sdk-for-go v19.1.0+incompatible/go.mod h1:9XXNKU+eRnpl9mo
 github.com/Azure/go-autorest v10.15.2+incompatible/go.mod h1:r+4oMnoxhatjLLJ6zxSWATqVooLgysK6ZNox3g/xq24=
 github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU=
 github.com/Microsoft/go-winio v0.4.5/go.mod h1:VhR8bwka0BXejwEJY73c50VrPtXAaKcyvVC4A4RozmA=
+github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af h1:wVe6/Ea46ZMeNkQjjBW6xcqyQA/j5e0D6GytH95g0gQ=
 github.com/ajstarks/svgo v0.0.0-20180226025133-644b8db467af/go.mod h1:K08gAheRH3/J6wwsYMMT4xOr94bZjxIelGM0+d/wbFw=
 github.com/alcortesm/tgz v0.0.0-20161220082320-9c5fe88206d7/go.mod h1:6zEj6s6u/ghQa61ZWa/C2Aw3RkjiTBOix7dkqa1VLIs=
 github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc=
@@ -43,6 +44,7 @@ github.com/docker/docker v1.4.2-0.20180109013817-94b8a116fbf1/go.mod h1:eEKB0N0r
 github.com/docker/go-connections v0.3.0/go.mod h1:Gbd7IOopHjR8Iph03tsViu4nIes5XhDvyHbTtUxmeec=
 github.com/docker/go-units v0.3.3-0.20171221200356-d59758554a3d/go.mod h1:fgPhTUdO+D/Jk86RDLlptpiXQzgHJF7gydDDbaIK4Dk=
 github.com/flynn/go-shlex v0.0.0-20150515145356-3f9db97f8568/go.mod h1:xEzjJPgXI435gkrCt3MPfRiAkVrwSbHsst4LCFVfpJc=
+github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90 h1:WXb3TSNmHp2vHoCroCIB1foO/yQ36swABL8aOVeDpgg=
 github.com/fogleman/gg v1.2.1-0.20190220221249-0403632d5b90/go.mod h1:R/bRT+9gY/C5z7JzPU0zXsXHKM4/ayA+zqcVNZzPa1k=
 github.com/fsnotify/fsnotify v1.4.9/go.mod h1:znqG4EE+3YCdAaPaxE2ZRY/06pZUdp0tY4IgpuI1SZQ=
 github.com/ghodss/yaml v1.0.0 h1:wQHKEahhL6wmXdzwWG11gIVCkOv05bNOh+Rxn0yngAk=
@@ -59,6 +61,7 @@ github.com/gogo/protobuf v1.1.1 h1:72R+M5VuhED/KujmZVcIquuo8mBgX4oVda//DQb3PXo=
 github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ=
 github.com/gogo/protobuf v1.3.1 h1:DqDEcV5aeaTmdFBePNpYsp3FlcVH/2ISVVM9Qf8PSls=
 github.com/gogo/protobuf v1.3.1/go.mod h1:SlYgWuQ5SjCEi6WLHjHCa1yvBfUnHcTbrrZtXPKa29o=
+github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0 h1:DACJavvAHhabrF08vX0COfcOBJRhZ8lUbR+ZWIs0Y5g=
 github.com/golang/freetype v0.0.0-20170609003504-e2365dfdc4a0/go.mod h1:E/TSTwGwJL78qG/PmXZO1EjYhfJinVAhrmmHX6Z8B9k=
 github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q=
 github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A=
@@ -107,6 +110,7 @@ github.com/json-iterator/go v1.1.7/go.mod h1:KdQUCv79m/52Kvf8AW2vK1V8akMuk1QjK/u
 github.com/json-iterator/go v1.1.9/go.mod h1:KdQUCv79m/52Kvf8AW2vK1V8akMuk1QjK/uOdHXbAo4=
 github.com/jstemmer/go-junit-report v0.0.0-20190106144839-af01ea7f8024/go.mod h1:6v2b51hI/fHJwM22ozAgKL4VKDeJcHhJFhtBdhmNjmU=
 github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7VTCxuUUipMqKk8s4w=
+github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5 h1:PJr+ZMXIecYc1Ey2zucXdR73SMBtgjPgwa31099IMv0=
 github.com/jung-kurt/gofpdf v1.0.3-0.20190309125859-24315acbbda5/go.mod h1:7Id9E/uU8ce6rXgefFLlgrJj/GYY22cpxn+r32jIOes=
 github.com/karalabe/xgo v0.0.0-20191115072854-c5ccff8648a7/go.mod h1:iYGcTYIPUvEWhFo6aKUuLchs+AV4ssYdyuBbQJZGcBk=
 github.com/kevinburke/ssh_config v0.0.0-20171013211458-802051befeb5/go.mod h1:CT57kijsi8u/K/BOFA39wgDQJ9CxiF4nAY/ojJ6r6mM=
@@ -203,6 +207,7 @@ golang.org/x/exp v0.0.0-20190121172915-509febef88a4 h1:c2HOrn5iMezYjSlGPncknSEr/
 golang.org/x/exp v0.0.0-20190121172915-509febef88a4/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
 golang.org/x/exp v0.0.0-20190125153040-c74c464bbbf2 h1:y102fOLFqhV41b+4GPiJoa0k/x+pJcEi2/HB1Y5T6fU=
 golang.org/x/exp v0.0.0-20190125153040-c74c464bbbf2/go.mod h1:CJ0aWSM057203Lf6IL+f9T1iT9GByDxfZKAQTCR3kQA=
+golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81 h1:00VmoueYNlNz/aHIilyyQz/MHSqGoWJzpFv/HW8xpzI=
 golang.org/x/image v0.0.0-20180708004352-c73c2afc3b81/go.mod h1:ux5Hcp/YLpHSI86hEcLt0YII63i6oz57MZXIpbrjZUs=
 golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE=
 golang.org/x/lint v0.0.0-20190227174305-5b3e6a55c961/go.mod h1:wehouNa3lNwaWXcvxsM5YxQ5yQlVC4a0KAMCusXpPoU=
@@ -267,6 +272,7 @@ gonum.org/v1/gonum v0.0.0-20180816165407-929014505bf4/go.mod h1:Y+Yx5eoAFn32cQvJ
 gonum.org/v1/gonum v0.8.1 h1:wGtP3yGpc5mCLOLeTeBdjeui9oZSz5De0eOjMLC/QuQ=
 gonum.org/v1/gonum v0.8.1/go.mod h1:oe/vMfY3deqTw+1EZJhuvEW2iwGF1bW9wwu7XCu0+v0=
 gonum.org/v1/netlib v0.0.0-20190313105609-8cb42192e0e0/go.mod h1:wa6Ws7BG/ESfp6dHfk7C6KdzKA7wR7u/rKwOGE66zvw=
+gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b h1:Qh4dB5D/WpoUUp3lSod7qgoyEHbDGPUWjIbnqdqqe1k=
 gonum.org/v1/plot v0.0.0-20190515093506-e2840ee46a6b/go.mod h1:Wt8AAjI+ypCyYX3nZBvf6cAIx93T+c/OS2HFAYskSZc=
 google.golang.org/api v0.4.0/go.mod h1:8k5glujaEP+g9n7WNsDg8QP6cUVNI86fCNMcbazEtwE=
 google.golang.org/api v0.13.0/go.mod h1:iLdEw5Ide6rF15KTC1Kkl0iskquN2gFfn9o9XIsbkAI=

diff --git a/import.go b/import.go
index aa83a70798c8a0c062a652a81afbbee24a761ecc..a43737232d06fb65816cb297f72e776b4d84de0f 100644 (file)
--- a/import.go
+++ b/import.go
@@ -8,6 +8,7 @@ import (
        "errors"
        "flag"
        "fmt"
+       "image/color/palette"
        "io"
        "net/http"
        _ "net/http/pprof"
@@ -24,6 +25,10 @@ import (
 
        "git.arvados.org/arvados.git/sdk/go/arvados"
        log "github.com/sirupsen/logrus"
+       "gonum.org/v1/plot"
+       "gonum.org/v1/plot/plotter"
+       "gonum.org/v1/plot/vg"
+       "gonum.org/v1/plot/vg/draw"
 )
 
 type importer struct {
@@ -497,3 +502,64 @@ func flatten(variants [][]tileVariantID) []tileVariantID {
        }
        return flat
 }
+
+type importstatsplot struct{}
+
+func (cmd *importstatsplot) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
+       err := cmd.Plot(stdin, stdout)
+       if err != nil {
+               log.Errorf("%s", err)
+               return 1
+       }
+       return 0
+}
+
+func (cmd *importstatsplot) Plot(stdin io.Reader, stdout io.Writer) error {
+       var stats []importStats
+       err := json.NewDecoder(stdin).Decode(&stats)
+       if err != nil {
+               return err
+       }
+
+       p, err := plot.New()
+       if err != nil {
+               return err
+       }
+       p.Title.Text = "coverage preserved by import (excl X<0.65)"
+       p.X.Label.Text = "input base calls ÷ sequence length"
+       p.Y.Label.Text = "output base calls ÷ input base calls"
+       p.Add(plotter.NewGrid())
+
+       data := map[string]plotter.XYs{}
+       for _, stat := range stats {
+               data[stat.InputLabel] = append(data[stat.InputLabel], plotter.XY{
+                       X: float64(stat.InputCoverage) / float64(stat.InputLength),
+                       Y: float64(stat.TileCoverage) / float64(stat.InputCoverage),
+               })
+       }
+
+       nextInPalette := 0
+       for label, xys := range data {
+               s, err := plotter.NewScatter(xys)
+               if err != nil {
+                       return err
+               }
+               s.GlyphStyle.Color = palette.Plan9[nextInPalette%len(palette.Plan9)]
+               s.GlyphStyle.Radius = vg.Millimeter / 2
+               s.GlyphStyle.Shape = draw.CrossGlyph{}
+               nextInPalette += 7
+               p.Add(s)
+               if false {
+                       p.Legend.Add(label, s)
+               }
+       }
+       p.X.Min = 0.65
+       p.X.Max = 1
+
+       w, err := p.WriterTo(8*vg.Inch, 6*vg.Inch, "svg")
+       if err != nil {
+               return err
+       }
+       _, err = w.WriteTo(stdout)
+       return err
+}