func printAllSubs(treeFile string) {
// Read the tree and get the sublineages.
tr, err := os.Open(treeFile)
defer tr.Close()
if err != nil {
log.Fatalf("subs: %v", err)
}
tree, err := devpat.ReadTree(tr)
if err != nil {
log.Fatalf("subs: reading tree: %v", err)
}
ts := devpat.AllSublineages(tree)
for _, t := range ts {
cs := make([]string, 0)
for c := range devpat.GetCells(t) {
cs = append(cs, c)
}
fmt.Println(strings.Join(cs, ","))
}
}
func codev(treeFile, cellTypeFile string, p float64, min int, notall bool) devpat.CoTypes {
// Read the tree and get the sublineages.
tr, err := os.Open(treeFile)
if err != nil {
log.Fatalf("codev: %v", err)
}
defer tr.Close()
tree, err := devpat.ReadTree(tr)
if err != nil {
log.Fatalf("codev: reading tree %v", err)
}
var ts []*devpat.Tree
if notall {
ts = devpat.Sublineages(tree, p, min)
} else {
ts = devpat.AllSublineages(tree)
}
// Get the cell to CellType mapping.
cr, err := os.Open(cellTypeFile)
if err != nil {
log.Fatalf("codev: %v", err)
}
defer cr.Close()
cts, err := devpat.ReadCellTypes(cr)
if err != nil {
log.Fatalf("codev: reading cell types: %v", err)
}
// Write the CellTypes in each sublineage.
var subFile string
if notall {
subFile = fmt.Sprintf("sublineages_%.0f_%d.csv", p, min)
} else {
subFile = "sublineages.csv"
}
subf, err := os.Create(subFile)
if err != nil {
log.Fatalf("codev: %v", err)
}
defer subf.Close()
err = devpat.WriteSublineageCellTypes(subf, ts, cts)
if err != nil {
log.Fatalf("codev: writing sublineage cell types: %v", err)
}
// Read the CellType sublineages.
subr, err := os.Open(subFile)
if err != nil {
log.Fatalf("codev: %v", err)
}
defer subr.Close()
subs, err := devpat.ReadCellTypeSublineages(subr)
if err != nil {
log.Fatalf("codev: reading cell type sublineages: %v", err)
}
return devpat.CodevScores(subs)
}
func fates(treeFile, xdatFile, markerFile string, cutoff, p float64, min int, all bool) {
tr, err := os.Open(treeFile)
defer tr.Close()
if err != nil {
log.Fatalf("fates: %v", err)
}
xs, err := devpat.ReadXDat(xdatFile)
if err != nil {
log.Fatalf("fates: %v", err)
}
mf, err := os.Open(markerFile)
defer mf.Close()
if err != nil {
log.Fatalf("fates: %v", err)
}
input := bufio.NewScanner(mf)
markers := make([]string, 0)
for input.Scan() {
markers = append(markers, input.Text())
}
if err := input.Err(); err != nil {
log.Fatalf("fates: %v", err)
}
tree, err := devpat.ReadTree(tr)
if err != nil {
log.Fatalf("fates: reading tree: %v", err)
}
var ts []*devpat.Tree
if all {
ts = devpat.AllSublineages(tree)
} else {
ts = devpat.Sublineages(tree, p, min)
}
fates := devpat.Fates(ts, xs, markers, cutoff)
// devpat.PrintFates(fates)
out, err := os.Create("fates.csv")
defer out.Close()
if err != nil {
log.Fatalf("fates: %v", err)
}
devpat.WriteFates(out, fates)
out, err = os.Create("sublineages.csv")
defer out.Close()
if err != nil {
log.Fatalf("fates: %v", err)
}
if _, err := fmt.Fprintln(out, "cell,sublineage"); err != nil {
log.Fatalf("fates: %v", err)
}
for i, t := range ts {
for c := range devpat.GetCells(t) {
_, err = fmt.Fprintf(out, "%s,%d\n", c, i)
if err != nil {
log.Fatalf("fates: %v", err)
}
}
}
}