Preserve pca components from input when writing samples.csv.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@curii.com>

diff --git a/slicenumpy.go b/slicenumpy.go
index 1c64744134ca1122173a2952a0754cddce8088a5..895c3c15fa2d91cfd7b153f65d6b78a9c59ad806 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -323,39 +323,9 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                cgnamemap[name] = true
        }
 
-       {
-               samplesOutFilename := *outputDir + "/samples.csv"
-               log.Infof("writing sample metadata to %s", samplesOutFilename)
-               var f *os.File
-               f, err = os.Create(samplesOutFilename)
-               if err != nil {
-                       return err
-               }
-               defer f.Close()
-               for i, si := range cmd.samples {
-                       var cc, tv string
-                       if si.isCase {
-                               cc = "1"
-                       } else if si.isControl {
-                               cc = "0"
-                       }
-                       if si.isTraining {
-                               tv = "1"
-                       } else if si.isValidation {
-                               tv = "0"
-                       }
-                       _, err = fmt.Fprintf(f, "%d,%s,%s,%s\n", i, si.id, cc, tv)
-                       if err != nil {
-                               err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
-                               return err
-                       }
-               }
-               err = f.Close()
-               if err != nil {
-                       err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
-                       return err
-               }
-               log.Print("done")
+       err = writeSampleInfo(cmd.samples, *outputDir)
+       if err != nil {
+               return err
        }
 
        log.Info("indexing reference tiles")
@@ -1288,50 +1258,19 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        }
                        log.Print("done")
 
-                       samplesOutFilename := *outputDir + "/samples.csv"
-                       log.Infof("writing sample metadata to %s", samplesOutFilename)
-                       var f *os.File
-                       f, err = os.Create(samplesOutFilename)
-                       if err != nil {
-                               return err
-                       }
-                       defer f.Close()
-                       pcaLabels := ""
-                       for i := 0; i < outcols; i++ {
-                               pcaLabels += fmt.Sprintf(",PCA%d", i)
-                       }
-                       _, err = fmt.Fprintf(f, "Index,SampleID,CaseControl,TrainingValidation%s\n", pcaLabels)
-                       if err != nil {
-                               return err
-                       }
-                       for i, si := range cmd.samples {
-                               var cc, tv string
-                               if si.isCase {
-                                       cc = "1"
-                               } else if si.isControl {
-                                       cc = "0"
-                               }
-                               if si.isTraining {
-                                       tv = "1"
-                               } else if si.isValidation {
-                                       tv = "0"
-                               }
-                               var pcavals string
+                       log.Print("copying pca components to sampleInfo")
+                       for i := range cmd.samples {
+                               cmd.samples[i].pcaComponents = make([]float64, outcols)
                                for c := 0; c < outcols; c++ {
-                                       pcavals += fmt.Sprintf(",%f", pca.At(i, c))
-                               }
-                               _, err = fmt.Fprintf(f, "%d,%s,%s,%s%s\n", i, si.id, cc, tv, pcavals)
-                               if err != nil {
-                                       err = fmt.Errorf("write %s: %w", samplesOutFilename, err)
-                                       return err
+                                       cmd.samples[i].pcaComponents[i] = pca.At(i, c)
                                }
                        }
-                       err = f.Close()
+                       log.Print("done")
+
+                       err = writeSampleInfo(cmd.samples, *outputDir)
                        if err != nil {
-                               err = fmt.Errorf("close %s: %w", samplesOutFilename, err)
                                return err
                        }
-                       log.Print("done")
                }
        }
        if !*mergeOutput && !*onehotChunked && !*onehotSingle && !*onlyPCA {
@@ -1420,13 +1359,60 @@ func loadSampleInfo(samplesFilename string) ([]sampleInfo, error) {
                        isCase:        split[2] == "1",
                        isControl:     split[2] == "0",
                        isTraining:    split[3] == "1",
-                       isValidation:  split[3] == "0",
+                       isValidation:  split[3] == "0" && len(split[2]) > 0, // fix errant 0s in input
                        pcaComponents: pcaComponents,
                })
        }
        return si, nil
 }
 
+func writeSampleInfo(samples []sampleInfo, outputDir string) error {
+       fnm := outputDir + "/samples.csv"
+       log.Infof("writing sample metadata to %s", fnm)
+       f, err := os.Create(fnm)
+       if err != nil {
+               return err
+       }
+       defer f.Close()
+       pcaLabels := ""
+       if len(samples) > 0 {
+               for i := range samples[0].pcaComponents {
+                       pcaLabels += fmt.Sprintf(",PCA%d", i)
+               }
+       }
+       _, err = fmt.Fprintf(f, "Index,SampleID,CaseControl,TrainingValidation%s\n", pcaLabels)
+       if err != nil {
+               return err
+       }
+       for i, si := range samples {
+               var cc, tv string
+               if si.isCase {
+                       cc = "1"
+               } else if si.isControl {
+                       cc = "0"
+               }
+               if si.isTraining {
+                       tv = "1"
+               } else if si.isValidation {
+                       tv = "0"
+               }
+               var pcavals string
+               for _, pcaval := range si.pcaComponents {
+                       pcavals += fmt.Sprintf(",%f", pcaval)
+               }
+               _, err = fmt.Fprintf(f, "%d,%s,%s,%s%s\n", i, si.id, cc, tv, pcavals)
+               if err != nil {
+                       return fmt.Errorf("write %s: %w", fnm, err)
+               }
+       }
+       err = f.Close()
+       if err != nil {
+               return fmt.Errorf("close %s: %w", fnm, err)
+       }
+       log.Print("done")
+       return nil
+}
+
 func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
        if cmd.chi2PValue >= 1 {
                return true