Logs.

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

diff --git a/pca.go b/pca.go
index 2bb8471d1b21112bd29ae7e166ec4ddd5f125732..d32751ea6d013a49386d3a6477f3bccc5ec664ae 100644 (file)
--- a/pca.go
+++ b/pca.go
@@ -137,6 +137,7 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
                }
                defer input.Close()
        }
+       log.Print("reading")
        cgs, err := ReadCompactGenomes(input)
        if err != nil {
                return 1
@@ -145,18 +146,23 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
        if err != nil {
                return 1
        }
+       log.Print("sorting")
        sort.Slice(cgs, func(i, j int) bool { return cgs[i].Name < cgs[j].Name })
 
+       log.Print("converting cgs to array")
        data, rows, cols := cgs2array(cgs)
        if *onehot {
                data, cols = recodeOnehot(data, cols)
        }
+       log.Print("running fit+transform")
        pca, err := nlp.NewPCA(*components).FitTransform(array2matrix(rows, cols, data).T())
        if err != nil {
                return 1
        }
 
+       log.Print("transposing result")
        pca = pca.T()
+       log.Print("copying result to numpy output array")
        rows, cols = pca.Dims()
        out := make([]float64, rows*cols)
        for i := 0; i < rows; i++ {
@@ -181,6 +187,7 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
                return 1
        }
        npw.Shape = []int{rows, cols}
+       log.Print("writing numpy")
        npw.WriteFloat64(out)
        err = bufw.Flush()
        if err != nil {
@@ -190,6 +197,7 @@ func (cmd *goPCA) RunCommand(prog string, args []string, stdin io.Reader, stdout
        if err != nil {
                return 1
        }
+       log.Print("done")
        return 0
 }