// XXX Temporary method to determine stable marker set.
func WriteToFile(statistics *genetic.MarkerStatistics) {
filename := "mutrates.txt"
minFreq := 1.0
nValuesMin := 1
nValuesMax := 5
stats := statistics.Select(minFreq, nValuesMin, nValuesMax)
err := ioutil.WriteFile(filename, []byte(stats.MutationRates()), os.ModePerm)
if err != nil {
fmt.Printf("Error writing mutation rates to file, %v.\r\n", err)
os.Exit(1)
}
}
func main() {
// Command line flags.
var (
treein = flag.String("treein", "", "Input filename for phylogenetic tree (.txt).")
treeout = flag.String("treeout", "", "Output filename for phylogenetic tree in TXT format.")
cal = flag.Float64("cal", 1, "Calibration factor for TMRCA calculation.")
offset = flag.Float64("offset", 0, "Offset is added to all calculated ages.")
personsin = flag.String("personsin", "", "Input filename (.txt or .csv) or directory.")
mrin = flag.String("mrin", "", "Filename for the import of mutation rates.")
gentime = flag.Float64("gentime", 1, "Generation time in years.")
inspect = flag.String("inspect", "", "Comma separated list of SNP names to search for.")
statistics = flag.Bool("statistics", false, "Prints marker statistics.")
method = flag.String("method", "parsimony", "Method to calculate modal haplotypes: phylofriend or parsimony.")
stage = flag.Int("stage", 4, "Processing stage for parsimony algorithm: 1, 2, 3, 4.")
trace = flag.String("trace", "", "Comma separated list of STR names to print out trace information.")
subclade = flag.String("subclade", "", "Selects a specific branch of the tree.")
htmlout = flag.String("htmlout", "", "Output filename for persons in HTML format.")
model = flag.String("model", "hybrid", "Mutation model: hybrid or infinite.")
)
flag.Parse()
var (
persons []*genetic.Person
mutationRates genetic.YstrMarkers
stat *genetic.MarkerStatistics
err error
)
// Load phylogenetic tree from file.
if *treein == "" {
fmt.Printf("No filename for input tree specified.\r\n")
os.Exit(1)
}
tree, err := phylotree.NewFromFile(*treein)
if err != nil {
fmt.Printf("Error reading tree from file, %v.\r\n", err)
os.Exit(1)
}
// Select subclade.
if *subclade != "" {
tree = tree.Subclade(*subclade)
if tree == nil {
fmt.Printf("Error, could not find specified subclade %s.\r\n", *subclade)
os.Exit(1)
}
}
// Read mutation rates from file.
if *mrin != "" {
mutationRates, err = genfiles.ReadMutationRates(*mrin)
if err != nil {
fmt.Printf("Error reading mutation rates %v.\r\n", err)
os.Exit(1)
}
} else {
// Use default values.
mutationRates = genetic.DefaultMutationRates()
}
// Load genetic sample results.
if *personsin != "" {
filenames := strings.Split(*personsin, ",")
for _, filename := range filenames {
var pers []*genetic.Person
fileInfo, err := os.Stat(filename)
switch {
case err != nil:
fmt.Printf("Error, something is wrong with personsin, %v.\r\n", err)
os.Exit(1)
case fileInfo.IsDir():
pers, err = genfiles.ReadPersonsFromDir(filename)
case strings.HasSuffix(strings.ToLower(filename), ".csv"):
pers, err = genfiles.ReadPersonsFromCSV(filename, 0)
default:
pers, err = genfiles.ReadPersonsFromTXT(filename)
}
if err != nil {
fmt.Printf("Error loading persons data %v.\r\n", err)
os.Exit(1)
}
persons = append(persons, pers...)
}
tree.InsertPersons(persons)
// Calculate marker statistics.
if *statistics == true || *method == "parsimony" {
stat = genetic.NewStatistics(persons)
}
// Print marker statistics.
if *statistics == true {
fmt.Print(stat.String())
// XXX Temporary code.
// WriteToFile(stat)
}
var isInfiniteAlleles bool
switch *model {
case "infinite":
isInfiniteAlleles = true
case "hybrid":
isInfiniteAlleles = false
default:
fmt.Printf("Error, unknown mutation model: %s.\n", *model)
os.Exit(1)
}
// Calculate modal haplotypes.
switch *method {
case "phylofriend":
tree.CalculateModalHaplotypes()
case "parsimony":
tree.CalculateModalHaplotypesParsimony(stat, *stage, isInfiniteAlleles)
default:
fmt.Printf("Error, unknown method %q to calculate modal haplotypes.\r\n", *method)
os.Exit(1)
}
if isInfiniteAlleles == true {
tree.CalculateDistances(mutationRates, genetic.DistanceInfiniteAlleles)
} else {
tree.CalculateDistances(mutationRates, genetic.DistanceHybrid)
}
}
// Calculate the age of this clade and all subclades.
// If the STR-Count is provided in the original tree input
// file the calculation can be performed even without sample
// data.
tree.CalculateAge(*gentime, *cal, *offset)
// Save resulting tree to file or print it out.
if *treeout != "" {
date := time.Now().Format("2006 Jan 2")
var buffer bytes.Buffer
buffer.WriteString("// This tree was created by the phyloage program: https://github.com/yogischogi/phyloage\r\n")
buffer.WriteString("// Command used:\r\n// ")
for _, arg := range os.Args {
buffer.WriteString(arg)
buffer.WriteString(" ")
}
buffer.WriteString("\r\n")
buffer.WriteString("// " + date + "\r\n\r\n")
buffer.WriteString(tree.String())
err := ioutil.WriteFile(*treeout, buffer.Bytes(), os.ModePerm)
if err != nil {
fmt.Printf("Error writing tree to file, %v.\r\n", err)
os.Exit(1)
}
} else {
fmt.Printf("%v\r\n", tree)
}
// Write Persons' Y-STR values in HTML format.
if *htmlout != "" {
persons := tree.Persons()
err = genfiles.WritePersonsAsHTML(*htmlout, persons, genetic.MaxMarkers)
if err != nil {
fmt.Printf("Error writing persons data to HTML file, %v.\n", err)
}
}
// Print tree with values of specified STRs.
if *trace != "" {
snps := strings.Split(*trace, ",")
fmt.Printf("%s", tree.Trace(snps))
}
// Search for SNPs and print out information about the matching subclades.
if *inspect != "" {
searchTerms := strings.Split(*inspect, ",")
fmt.Printf("%s", tree.Inspect(searchTerms))
}
}