Updating lightning Dockerfile to go from `pip3 install sklearn` -> `pip3 install...

[lightning.git] / slicenumpy.go

diff --git a/slicenumpy.go b/slicenumpy.go
index 90a062cbbb1d4ff2f82ad7da073c47af9140c9e6..5b55070679f57dee11adf420f0bdcced353dbdd8 100644 (file)
--- a/slicenumpy.go
+++ b/slicenumpy.go
@@ -45,6 +45,7 @@ type sliceNumpy struct {
        chi2Cases          []bool
        chi2PValue         float64
        pvalueMinFrequency float64
+       maxFrequency       float64
        pcaComponents      int
        minCoverage        int
        includeVariant1    bool
@@ -96,6 +97,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
        flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads, and number of VCPUs to request for arvados container")
        flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test (or logistic regression if -samples file has PCA components) and omit columns with p-value above this threshold")
        flags.Float64Var(&cmd.pvalueMinFrequency, "pvalue-min-frequency", 0.01, "skip p-value calculation on tile variants below this frequency in the training set")
+       flags.Float64Var(&cmd.maxFrequency, "max-frequency", 1, "do not output variants above this frequency in the training set")
        flags.BoolVar(&cmd.includeVariant1, "include-variant-1", false, "include most common variant when building one-hot matrix")
        cmd.filter.Flags(flags)
        err := flags.Parse(args)
@@ -154,6 +156,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        "-max-pca-tiles=" + fmt.Sprintf("%d", *maxPCATiles),
                        "-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
                        "-pvalue-min-frequency=" + fmt.Sprintf("%f", cmd.pvalueMinFrequency),
+                       "-max-frequency=" + fmt.Sprintf("%f", cmd.maxFrequency),
                        "-include-variant-1=" + fmt.Sprintf("%v", cmd.includeVariant1),
                        "-debug-tag=" + fmt.Sprintf("%d", cmd.debugTag),
                }
@@ -528,7 +531,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        if err == errSkip {
                                return nil
                        } else if err != nil {
-                               return fmt.Errorf("%04d: DecodeLibrary(%s): err", infileIdx, infile)
+                               return fmt.Errorf("%04d: DecodeLibrary(%s): %w", infileIdx, infile, err)
                        }
                        tagstart := cgs[cmd.cgnames[0]].StartTag
                        tagend := cgs[cmd.cgnames[0]].EndTag
@@ -1265,7 +1268,7 @@ func (cmd *sliceNumpy) run(prog string, args []string, stdin io.Reader, stdout,
                        for i := range cmd.samples {
                                cmd.samples[i].pcaComponents = make([]float64, outcols)
                                for c := 0; c < outcols; c++ {
-                                       cmd.samples[i].pcaComponents[i] = pca.At(i, c)
+                                       cmd.samples[i].pcaComponents[c] = pca.At(i, c)
                                }
                        }
                        log.Print("done")
@@ -1646,12 +1649,18 @@ func (cmd *sliceNumpy) tv2homhet(cgs map[string]CompactGenome, maxv tileVariantI
                }
                if col&1 == 0 {
                        maf = homhet2maf(obs[col : col+2])
-                       if cmd.pvalueMinFrequency < 1 && maf < cmd.pvalueMinFrequency {
+                       if maf < cmd.pvalueMinFrequency {
                                // Skip both columns (hom and het) if
                                // allele frequency is below threshold
                                col++
                                continue
                        }
+                       if maf > cmd.maxFrequency {
+                               // Skip both columns if allele
+                               // frequency is above threshold
+                               col++
+                               continue
+                       }
                }
                atomic.AddInt64(&cmd.pvalueCallCount, 1)
                p := cmd.pvalue(obs[col])