Seed as root option, with only '--seed'

evolbioinfo · Sep 21, 2018 · a3ae4f1 · a3ae4f1
1 parent d6db0ae
commit a3ae4f1
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Showing 18 changed files with 67 additions and 121 deletions.
diff --git a/cmd/acr.go b/cmd/acr.go
@@ -6,11 +6,9 @@ import (
 	"errors"
 	"fmt"
 	goio "io"
-	"math/rand"
 	"os"
 	"regexp"
 	"strings"
-	"time"
 
 	"github.com/fredericlemoine/gotree/acr"
 	"github.com/fredericlemoine/gotree/io"
@@ -50,8 +48,6 @@ randomly before going deeper in the tree.
 		var treechan <-chan tree.Trees
 		var f *os.File
 
-		rand.Seed(seed)
-
 		switch strings.ToLower(parsimonyAlgo) {
 		case "acctran":
 			algo = acr.ALGO_ACCTRAN
@@ -117,8 +113,6 @@ func init() {
 	acrCmd.PersistentFlags().StringVar(&outresfile, "out-states", "none", "Output mapping file between node names and states")
 	acrCmd.PersistentFlags().StringVar(&parsimonyAlgo, "algo", "acctran", "Parsimony algorithm for resolving ambiguities: acctran, deltran, or downpass")
 	acrCmd.PersistentFlags().BoolVar(&acrrandomresolve, "random-resolve", false, "Random resolve states when several possibilities in: acctran, deltran, or downpass")
-	acrCmd.Flags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
-
 }
 
 func parseTipStates(file string) (states map[string]string, err error) {

diff --git a/cmd/asr.go b/cmd/asr.go
@@ -4,10 +4,8 @@ import (
 	"bufio"
 	"fmt"
 	goio "io"
-	"math/rand"
 	"os"
 	"strings"
-	"time"
 
 	"github.com/fredericlemoine/goalign/align"
 	"github.com/fredericlemoine/goalign/io/fasta"
@@ -53,8 +51,6 @@ randomly before going deeper in the tree.
 		var treechan <-chan tree.Trees
 		var f *os.File
 
-		rand.Seed(seed)
-
 		switch strings.ToLower(parsimonyAlgo) {
 		case "acctran":
 			algo = asr.ALGO_ACCTRAN
@@ -126,5 +122,4 @@ func init() {
 	asrCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "Output file")
 	asrCmd.PersistentFlags().StringVar(&parsimonyAlgo, "algo", "acctran", "Parsimony algorithm for resolving ambiguities: acctran, deltran, or downpass")
 	asrCmd.PersistentFlags().BoolVar(&asrrandomresolve, "random-resolve", false, "Random resolve states when several possibilities in: acctran, deltran, or downpass")
-	asrCmd.Flags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 }
diff --git a/cmd/balancedtree.go b/cmd/balancedtree.go
@@ -1,20 +1,18 @@
 package cmd
 
 import (
+	"os"
+
 	"github.com/fredericlemoine/gotree/io"
 	"github.com/fredericlemoine/gotree/tree"
 	"github.com/spf13/cobra"
-	"math/rand"
-	"os"
 )
 
-func balancedTree(nbtrees int, depth int, output string, seed int64, rooted bool) error {
+func balancedTree(nbtrees int, depth int, output string, rooted bool) error {
 	var f *os.File
 	var err error
 	var t *tree.Tree
 
-	rand.Seed(seed)
-
 	if output != "stdout" && output != "-" {
 		f, err = os.Create(output)
 		defer f.Close()
@@ -42,7 +40,7 @@ var balancedtreeCmd = &cobra.Command{
 	Long: `Generates a random balanced binary tree
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
-		if err = balancedTree(generateNbTrees, generateDepth, generateOutputfile, generateSeed, generateRooted); err != nil {
+		if err = balancedTree(generateNbTrees, generateDepth, generateOutputfile, generateRooted); err != nil {
 			io.LogError(err)
 		}
 		return

diff --git a/cmd/booster.go b/cmd/booster.go
@@ -3,7 +3,6 @@ package cmd
 import (
 	"fmt"
 	goio "io"
-	"math/rand"
 	"time"
 
 	"github.com/fredericlemoine/gotree/io"
@@ -24,7 +23,6 @@ var boosterCmd = &cobra.Command{
 		var boottreechan <-chan tree.Trees
 
 		writeLogBooster()
-		rand.Seed(seed)
 		if refTree, err = readTree(supportIntree); err != nil {
 			io.LogError(err)
 			return
@@ -62,7 +60,6 @@ func init() {
 	boosterCmd.PersistentFlags().BoolVar(&hightaxperbranches, "highest-per-branches", false, "If true, will print in log file (-l) average taxa transfers for highly transfered taxa per banches of the reference tree (i.e. the x most transfered, with x~ average distance)")
 	boosterCmd.PersistentFlags().StringVarP(&rawSupportOutputFile, "out-raw", "r", "none", "If given, then prints the same tree with non normalized supports (average transfer distance) as branch names, in the form branch_id|avg_distance|branch_depth")
 	boosterCmd.PersistentFlags().Float64Var(&cutoff, "dist-cutoff", 0.3, "If --moved-taxa, then this is the distance cutoff to consider a branch for moving taxa computation. It is the normalized distance to the current bootstrap tree (e.g. 0.05). Must be between 0 and 1, otherwise set to 0")
-	boosterCmd.PersistentFlags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed if empirical is ON")
 }
 
 func writeLogBooster() {
@@ -71,6 +68,5 @@ func writeLogBooster() {
 	supportLog.WriteString(fmt.Sprintf("Input tree  : %s\n", supportIntree))
 	supportLog.WriteString(fmt.Sprintf("Boot trees  : %s\n", supportBoottrees))
 	supportLog.WriteString(fmt.Sprintf("Output tree : %s\n", supportOutFile))
-	supportLog.WriteString(fmt.Sprintf("Seed        : %d\n", seed))
 	supportLog.WriteString(fmt.Sprintf("CPUs        : %d\n", rootCpus))
 }
diff --git a/cmd/caterpillartree.go b/cmd/caterpillartree.go
@@ -1,20 +1,18 @@
 package cmd
 
 import (
+	"os"
+
 	"github.com/fredericlemoine/gotree/io"
 	"github.com/fredericlemoine/gotree/tree"
 	"github.com/spf13/cobra"
-	"math/rand"
-	"os"
 )
 
-func caterpilarTree(nbtrees int, nbtips int, output string, seed int64, rooted bool) error {
+func caterpilarTree(nbtrees int, nbtips int, output string, rooted bool) error {
 	var f *os.File
 	var err error
 	var t *tree.Tree
 
-	rand.Seed(seed)
-
 	if output != "stdout" && output != "-" {
 		f, err = os.Create(output)
 		defer f.Close()
@@ -41,7 +39,7 @@ var caterpilartreeCmd = &cobra.Command{
 	Short: "Generates a random caterpilar binary tree",
 	Long:  `Generates a random caterpilar binary tree.`,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
-		if err = caterpilarTree(generateNbTrees, generateNbTips, generateOutputfile, generateSeed, generateRooted); err != nil {
+		if err = caterpilarTree(generateNbTrees, generateNbTips, generateOutputfile, generateRooted); err != nil {
 			io.LogError(err)
 		}
 		return

diff --git a/cmd/generate.go b/cmd/generate.go
@@ -2,14 +2,12 @@ package cmd
 
 import (
 	"github.com/spf13/cobra"
-	"time"
 )
 
 var generateNbTips int
 var generateDepth int
 var generateNbTrees int
 var generateOutputfile string
-var generateSeed int64
 var generateRooted bool
 
 // generateCmd represents the generate command
@@ -23,7 +21,6 @@ var generateCmd = &cobra.Command{
 func init() {
 	RootCmd.AddCommand(generateCmd)
 	generateCmd.PersistentFlags().IntVarP(&generateNbTrees, "nbtrees", "n", 1, "Number of trees to generate")
-	generateCmd.PersistentFlags().Int64VarP(&generateSeed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 	generateCmd.PersistentFlags().StringVarP(&generateOutputfile, "output", "o", "stdout", "Number of tips of the tree to generate")
 	generateCmd.PersistentFlags().BoolVarP(&generateRooted, "rooted", "r", false, "Generate rooted trees")
 }
diff --git a/cmd/prune.go b/cmd/prune.go
@@ -4,7 +4,6 @@ import (
 	goio "io"
 	"math/rand"
 	"os"
-	"time"
 
 	"github.com/fredericlemoine/gotree/io"
 	"github.com/fredericlemoine/gotree/tree"
@@ -89,7 +88,6 @@ If -r is given, behavior is reversed, it keep given tips instead of removing the
 		var treechan <-chan tree.Trees
 
 		var specificTipNames []string
-		rand.Seed(seed)
 
 		if f, err = openWriteFile(outtreefile); err != nil {
 			io.LogError(err)
@@ -147,6 +145,5 @@ func init() {
 	pruneCmd.Flags().StringVarP(&outtreefile, "output", "o", "stdout", "Output tree")
 	pruneCmd.Flags().StringVarP(&tipfile, "tipfile", "f", "none", "Tip file")
 	pruneCmd.Flags().BoolVarP(&revert, "revert", "r", false, "If true, then revert the behavior: will keep only species given in the command line, or keep only the species that are specific to the input tree, or keep only randomly selected taxa")
-	pruneCmd.PersistentFlags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 	pruneCmd.PersistentFlags().IntVar(&randomtips, "random", 0, "Number of tips to randomly sample")
 }
diff --git a/cmd/randbrlen.go b/cmd/randbrlen.go
@@ -2,9 +2,7 @@ package cmd
 
 import (
 	goio "io"
-	"math/rand"
 	"os"
-	"time"
 
 	"github.com/fredericlemoine/gostats"
 	"github.com/fredericlemoine/gotree/io"
@@ -23,10 +21,6 @@ var randbrlenCmd = &cobra.Command{
 Length follows an exponential distribution of parameter lambda=1/0.1 
 (Mean=0.1)
 `,
-	PersistentPreRun: func(cmd *cobra.Command, args []string) {
-		RootCmd.PersistentPreRun(cmd, args)
-		rand.Seed(seed)
-	},
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
 		var treefile goio.Closer
@@ -63,7 +57,6 @@ func init() {
 	brlenCmd.AddCommand(randbrlenCmd)
 
 	randbrlenCmd.PersistentFlags().StringVarP(&intreefile, "input", "i", "stdin", "Input tree")
-	randbrlenCmd.Flags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 	randbrlenCmd.Flags().Float64VarP(&setlengthmean, "mean", "m", 0.1, "Mean of the exponential distribution of branch lengths")
 	randbrlenCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "Random length output tree file")
 }
diff --git a/cmd/randsupport.go b/cmd/randsupport.go
@@ -2,9 +2,7 @@ package cmd
 
 import (
 	goio "io"
-	"math/rand"
 	"os"
-	"time"
 
 	"github.com/fredericlemoine/gostats"
 	"github.com/fredericlemoine/gotree/io"
@@ -21,10 +19,6 @@ var randsupportCmd = &cobra.Command{
 Support follows a uniform distribution in [0,1].
 
 `,
-	PersistentPreRun: func(cmd *cobra.Command, args []string) {
-		RootCmd.PersistentPreRun(cmd, args)
-		rand.Seed(seed)
-	},
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var f *os.File
 		var treefile goio.Closer
@@ -63,5 +57,4 @@ func init() {
 
 	randsupportCmd.PersistentFlags().StringVarP(&intreefile, "input", "i", "stdin", "Input tree")
 	randsupportCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "Output file")
-	randsupportCmd.Flags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 }
diff --git a/cmd/resolve.go b/cmd/resolve.go
@@ -2,9 +2,7 @@ package cmd
 
 import (
 	goio "io"
-	"math/rand"
 	"os"
-	"time"
 
 	"github.com/fredericlemoine/gotree/io"
 	"github.com/fredericlemoine/gotree/tree"
@@ -26,7 +24,6 @@ var resolveCmd = &cobra.Command{
 		var treefile goio.Closer
 		var treechan <-chan tree.Trees
 
-		rand.Seed(seed)
 		if f, err = openWriteFile(outtreefile); err != nil {
 			io.LogError(err)
 			return
@@ -55,5 +52,4 @@ func init() {
 	RootCmd.AddCommand(resolveCmd)
 	resolveCmd.PersistentFlags().StringVarP(&intreefile, "input", "i", "stdin", "Input tree(s) file")
 	resolveCmd.PersistentFlags().StringVarP(&outtreefile, "output", "o", "stdout", "Resolved tree(s) output file")
-	resolveCmd.PersistentFlags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 }
diff --git a/cmd/root.go b/cmd/root.go
@@ -6,10 +6,12 @@ import (
 	"errors"
 	"fmt"
 	goio "io"
+	"math/rand"
 	"os"
 	"runtime"
 	"strconv"
 	"strings"
+	"time"
 
 	"github.com/fredericlemoine/cobrashell"
 	"github.com/fredericlemoine/gotree/io/fileutils"
@@ -22,7 +24,7 @@ import (
 var inalignfile string
 var intreefile, intree2file, outtreefile string
 var outresfile string
-var seed int64
+var seed int64 = -1
 var inputname string
 var mapfile string
 var revert bool
@@ -64,6 +66,10 @@ Different usages are implemented:
 		default:
 			treeformat = utils.FORMAT_NEWICK
 		}
+		if seed == -1 {
+			seed = time.Now().UTC().UnixNano()
+		}
+		rand.Seed(seed)
 	},
 
 	Run: func(cmd *cobra.Command, args []string) {
@@ -92,8 +98,8 @@ func Execute() {
 func init() {
 	cobra.OnInitialize(initConfig)
 	maxcpus := runtime.NumCPU()
-	//RootCmd.AddCommand(krait.NewConsoleCommand())
 
+	RootCmd.PersistentFlags().Int64Var(&seed, "seed", -1, "Random Seed: -1 = nano seconds since 1970/01/01 00:00:00")
 	RootCmd.PersistentFlags().IntVarP(&rootCpus, "threads", "t", 1, "Number of threads (Max="+strconv.Itoa(maxcpus)+")")
 	RootCmd.PersistentFlags().StringVar(&rootInputFormat, "format", "newick", "Input tree format (newick, nexus, or phyloxml)")
 }

diff --git a/cmd/rotate_rand.go b/cmd/rotate_rand.go
@@ -2,9 +2,7 @@ package cmd
 
 import (
 	goio "io"
-	"math/rand"
 	"os"
-	"time"
 
 	"github.com/fredericlemoine/gotree/io"
 	"github.com/fredericlemoine/gotree/tree"
@@ -36,7 +34,6 @@ gotree rotate rand -i t.nw
 		var treechan <-chan tree.Trees
 
 		// Read Tree
-		rand.Seed(seed)
 		if f, err = openWriteFile(outtreefile); err != nil {
 			io.LogError(err)
 			return
@@ -62,5 +59,4 @@ gotree rotate rand -i t.nw
 
 func init() {
 	rotateCmd.AddCommand(rotateRandCmd)
-	rotateRandCmd.Flags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 }
diff --git a/cmd/rotate_sort.go b/cmd/rotate_sort.go
@@ -2,7 +2,6 @@ package cmd
 
 import (
 	goio "io"
-	"math/rand"
 	"os"
 
 	"github.com/fredericlemoine/gotree/io"
@@ -35,7 +34,6 @@ gotree rotate sort -i t.nw
 		var treechan <-chan tree.Trees
 
 		// Read Tree
-		rand.Seed(seed)
 		if f, err = openWriteFile(outtreefile); err != nil {
 			io.LogError(err)
 			return

diff --git a/cmd/sample.go b/cmd/sample.go
@@ -4,7 +4,6 @@ import (
 	goio "io"
 	"math/rand"
 	"os"
-	"time"
 
 	"github.com/fredericlemoine/gotree/io"
 	"github.com/fredericlemoine/gotree/tree"
@@ -32,7 +31,6 @@ If the number of desired trees is > number of input trees:
 
 		totaltrees := 0
 		outtrees := make([]*tree.Tree, numtrees)
-		rand.Seed(seed)
 
 		if treefile, treechan, err = readTrees(intreefile); err != nil {
 			io.LogError(err)
@@ -98,6 +96,5 @@ func init() {
 	sampleCmd.Flags().StringVarP(&intreefile, "input", "i", "stdin", "Input reference trees")
 	sampleCmd.Flags().StringVarP(&outtreefile, "output", "o", "stdout", "Output trees")
 	sampleCmd.PersistentFlags().IntVarP(&numtrees, "nbtrees", "n", 1, "Number of trees to sample from input file")
-	sampleCmd.PersistentFlags().Int64VarP(&seed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 	sampleCmd.PersistentFlags().BoolVar(&replace, "replace", false, "If given, samples with replacement")
 }