c.Log("=== slice-numpy + chunked hgvs matrix ===")
{
- err = ioutil.WriteFile(tmpdir+"/cases.txt", []byte("pipeline1/input1\npipeline1dup/input1\n"), 0600)
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+pipeline1/input1 1
+pipeline1/input2 0
+pipeline1dup/input1 1
+pipeline1dup/input2 0
+`), 0600)
c.Assert(err, check.IsNil)
npydir := c.MkDir()
exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-hgvs-matrix=true",
- "-chi2-cases-file=" + tmpdir + "/cases.txt",
+ "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-chi2-case-control-column=CC",
"-chi2-p-value=0.05",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
c.Log("=== slice-numpy + onehot ===")
{
- err = ioutil.WriteFile(tmpdir+"/cases.txt", []byte("pipeline1/input1\npipeline1dup/input1\n"), 0600)
+ err = ioutil.WriteFile(tmpdir+"/casecontrol.tsv", []byte(`SampleID CC
+pipeline1/input1 1
+pipeline1/input2 0
+pipeline1dup/input1 1
+pipeline1dup/input2 0
+`), 0600)
c.Assert(err, check.IsNil)
npydir := c.MkDir()
exited := (&sliceNumpy{}).RunCommand("slice-numpy", []string{
"-local=true",
"-chunked-onehot=true",
- "-chi2-cases-file=" + tmpdir + "/cases.txt",
+ "-chi2-case-control-file=" + tmpdir + "/casecontrol.tsv",
+ "-chi2-case-control-column=CC",
"-chi2-p-value=0.05",
"-min-coverage=0.75",
"-input-dir=" + slicedir,
)
type sliceNumpy struct {
- filter filter
- threads int
- chi2CasesFile string
- chi2Cases []bool
- chi2PValue float64
- minCoverage int
- cgnames []string
+ filter filter
+ threads int
+ chi2CaseControlColumn string
+ chi2CaseControlFile string
+ chi2Cases []bool
+ chi2PValue float64
+ minCoverage int
+ cgnames []string
}
func (cmd *sliceNumpy) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
hgvsChunked := flags.Bool("chunked-hgvs-matrix", false, "also generate hgvs-based matrix per chromosome")
onehotChunked := flags.Bool("chunked-onehot", false, "generate one-hot tile-based matrix")
flags.IntVar(&cmd.threads, "threads", 16, "number of memory-hungry assembly threads")
- flags.StringVar(&cmd.chi2CasesFile, "chi2-cases-file", "", "text file indicating positive cases (for Χ² test)")
+ flags.StringVar(&cmd.chi2CaseControlFile, "chi2-case-control-file", "", "tsv file or directory indicating cases and controls for Χ² test (if directory, all .tsv files will be read)")
+ flags.StringVar(&cmd.chi2CaseControlColumn, "chi2-case-control-column", "", "name of case/control column in case-control files for Χ² test (value must be 0 for control, 1 for case)")
flags.Float64Var(&cmd.chi2PValue, "chi2-p-value", 1, "do Χ² test and omit columns with p-value above this threshold")
cmd.filter.Flags(flags)
err = flags.Parse(args)
}()
}
- if cmd.chi2CasesFile == "" && cmd.chi2PValue != 1 {
- log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-cases-file= value is empty", cmd.chi2PValue)
+ if cmd.chi2PValue != 1 && (cmd.chi2CaseControlFile == "" || cmd.chi2CaseControlColumn == "") {
+ log.Errorf("cannot use provided -chi2-p-value=%f because -chi2-case-control-file= or -chi2-case-control-column= value is empty", cmd.chi2PValue)
return 2
}
KeepCache: 2,
APIAccess: true,
}
- err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CasesFile)
+ err = runner.TranslatePaths(inputDir, regionsFilename, &cmd.chi2CaseControlFile)
if err != nil {
return 1
}
"-single-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsSingle),
"-chunked-hgvs-matrix=" + fmt.Sprintf("%v", *hgvsChunked),
"-chunked-onehot=" + fmt.Sprintf("%v", *onehotChunked),
- "-chi2-cases-file=" + cmd.chi2CasesFile,
+ "-chi2-case-control-file=" + cmd.chi2CaseControlFile,
+ "-chi2-case-control-column=" + cmd.chi2CaseControlColumn,
"-chi2-p-value=" + fmt.Sprintf("%f", cmd.chi2PValue),
}
runner.Args = append(runner.Args, cmd.filter.Args()...)
return 0
}
- infiles, err := allGobFiles(*inputDir)
+ infiles, err := allFiles(*inputDir, matchGobFile)
if err != nil {
return 1
}
return 1
}
sort.Strings(cmd.cgnames)
-
- cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
-
- if cmd.chi2CasesFile != "" {
- f, err2 := open(cmd.chi2CasesFile)
- if err2 != nil {
- err = err2
- return 1
- }
- buf, err2 := io.ReadAll(f)
- f.Close()
- if err2 != nil {
- err = err2
- return 1
- }
- cmd.chi2Cases = make([]bool, len(cmd.cgnames))
- ncases := 0
- for _, pattern := range bytes.Split(buf, []byte{'\n'}) {
- if len(pattern) == 0 {
- continue
- }
- pattern := string(pattern)
- idx := -1
- for i, name := range cmd.cgnames {
- if !strings.Contains(name, pattern) {
- continue
- }
- cmd.chi2Cases[i] = true
- ncases++
- if idx >= 0 {
- log.Warnf("pattern %q in cases file matches multiple genome IDs: %q, %q", pattern, cmd.cgnames[idx], name)
- } else {
- idx = i
- }
- }
- if idx < 0 {
- log.Warnf("pattern %q in cases file does not match any genome IDs", pattern)
- continue
- }
- }
- log.Printf("%d cases, %d controls", ncases, len(cmd.cgnames)-ncases)
+ err = cmd.useCaseControlFiles()
+ if err != nil {
+ return 1
}
+ cmd.minCoverage = int(math.Ceil(cmd.filter.MinCoverage * float64(len(cmd.cgnames))))
{
- labelsFilename := *outputDir + "/labels.csv"
+ labelsFilename := *outputDir + "/samples.csv"
log.Infof("writing labels to %s", labelsFilename)
var f *os.File
f, err = os.Create(labelsFilename)
}
defer f.Close()
for i, name := range cmd.cgnames {
- _, err = fmt.Fprintf(f, "%d,%q\n", i, trimFilenameForLabel(name))
+ cc := 0
+ if cmd.chi2Cases != nil && cmd.chi2Cases[i] {
+ cc = 1
+ }
+ _, err = fmt.Fprintf(f, "%d,%q,%d\n", i, trimFilenameForLabel(name), cc)
if err != nil {
err = fmt.Errorf("write %s: %w", labelsFilename, err)
return 1
return 0
}
+// Read case/control files, remove non-case/control entries from
+// cmd.cgnames, and build cmd.chi2Cases.
+func (cmd *sliceNumpy) useCaseControlFiles() error {
+ if cmd.chi2CaseControlFile == "" {
+ return nil
+ }
+ infiles, err := allFiles(cmd.chi2CaseControlFile, nil)
+ if err != nil {
+ return err
+ }
+ // index in cmd.cgnames => case(true) / control(false)
+ cc := map[int]bool{}
+ for _, infile := range infiles {
+ f, err := open(infile)
+ if err != nil {
+ return err
+ }
+ buf, err := io.ReadAll(f)
+ f.Close()
+ if err != nil {
+ return err
+ }
+ ccCol := -1
+ for _, tsv := range bytes.Split(buf, []byte{'\n'}) {
+ if len(tsv) == 0 {
+ continue
+ }
+ split := strings.Split(string(tsv), "\t")
+ if ccCol < 0 {
+ // header row
+ for col, name := range split {
+ if name == cmd.chi2CaseControlColumn {
+ ccCol = col
+ break
+ }
+ }
+ if ccCol < 0 {
+ return fmt.Errorf("%s: no column named %q in header row %q", infile, cmd.chi2CaseControlColumn, tsv)
+ }
+ continue
+ }
+ if len(split) <= ccCol {
+ continue
+ }
+ pattern := split[0]
+ found := -1
+ for i, name := range cmd.cgnames {
+ if strings.Contains(name, pattern) {
+ if found >= 0 {
+ log.Warnf("pattern %q in %s matches multiple genome IDs (%qs, %q)", pattern, infile, cmd.cgnames[found], name)
+ }
+ found = i
+ }
+ }
+ if found < 0 {
+ log.Warnf("pattern %q in %s does not match any genome IDs", pattern, infile)
+ continue
+ }
+ if split[ccCol] == "0" {
+ cc[found] = false
+ }
+ if split[ccCol] == "1" {
+ cc[found] = true
+ }
+ }
+ }
+ allnames := cmd.cgnames
+ cmd.cgnames = nil
+ cmd.chi2Cases = nil
+ ncases := 0
+ for i, name := range allnames {
+ if cc, ok := cc[i]; ok {
+ cmd.cgnames = append(cmd.cgnames, name)
+ cmd.chi2Cases = append(cmd.chi2Cases, cc)
+ if cc {
+ ncases++
+ }
+ }
+ }
+ log.Printf("%d cases, %d controls, %d neither (dropped)", ncases, len(cmd.cgnames)-ncases, len(allnames)-len(cmd.cgnames))
+ return nil
+}
+
func (cmd *sliceNumpy) filterHGVScolpair(colpair [2][]int8) bool {
if cmd.chi2PValue >= 1 {
return true
projects / lightning.git / commitdiff