Changed sample commands

cmd/sample.go

@@ -1,46 +1,24 @@
 package cmd
 
 import (
-	"github.com/fredericlemoine/goalign/io"
 	"github.com/spf13/cobra"
-	"math/rand"
-	"time"
 )
 
-var sampleSeed int64
-var sampleOutput string
-var sampleNb int
-
 // sampleCmd represents the sample command
 var sampleCmd = &cobra.Command{
 	Use:   "sample",
-	Short: "Samples a subset of sequences from the input alignment",
-	Long: `Samples a subset of sequences from the input alignment.
-
-May take a Fasta or Phylip alignment in input.
+	Short: "Samples sequences or sites from an input alignment",
+	Long: `Samples sequences or sites from an input alignment. For example:
 
-If the input alignment contains several alignments, will process all of them
+Randomly sampling 10 sequences from the alignment:
+goalign sample seqs -i align.fa -n 10 > sample.fa
 
-As output, writes an alignment containing a sample of the sequences
+Randomly sampling 10 subsequences with length 20 from the input alignment:
+goalign sample seqs -n 10 -i align.fa -l 20 -o subalign_
 
 `,
-	Run: func(cmd *cobra.Command, args []string) {
-		rand.Seed(sampleSeed)
-		f := openWriteFile(sampleOutput)
-		for al := range rootaligns {
-			if sample, err := al.Sample(sampleNb); err != nil {
-				io.ExitWithMessage(err)
-			} else {
-				writeAlign(sample, f)
-			}
-		}
-		f.Close()
-	},
 }
 
 func init() {
 	RootCmd.AddCommand(sampleCmd)
-	sampleCmd.PersistentFlags().IntVarP(&sampleNb, "nb-seq", "n", 1, "Number of sequences to sample from the alignment")
-	sampleCmd.PersistentFlags().Int64VarP(&sampleSeed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
-	sampleCmd.PersistentFlags().StringVarP(&sampleOutput, "output", "o", "stdout", "Sampled alignment output file")
 }

cmd/sampleseq.go

@@ -0,0 +1,46 @@
+package cmd
+
+import (
+	"github.com/fredericlemoine/goalign/io"
+	"github.com/spf13/cobra"
+	"math/rand"
+	"time"
+)
+
+var sampleseqSeed int64
+var sampleseqOutput string
+var sampleseqNb int
+
+// sampleCmd represents the sample command
+var sampleseqCmd = &cobra.Command{
+	Use:   "seqs",
+	Short: "Samples a subset of sequences from the input alignment",
+	Long: `Samples a subset of sequences from the input alignment.
+
+May take a Fasta or Phylip alignment in input.
+
+If the input alignment contains several alignments, will process all of them
+
+As output, writes an alignment containing a sample of the sequences
+
+`,
+	Run: func(cmd *cobra.Command, args []string) {
+		rand.Seed(sampleseqSeed)
+		f := openWriteFile(sampleseqOutput)
+		for al := range rootaligns {
+			if sample, err := al.Sample(sampleseqNb); err != nil {
+				io.ExitWithMessage(err)
+			} else {
+				writeAlign(sample, f)
+			}
+		}
+		f.Close()
+	},
+}
+
+func init() {
+	sampleCmd.AddCommand(sampleseqCmd)
+	sampleseqCmd.PersistentFlags().IntVarP(&sampleseqNb, "nb-seq", "n", 1, "Number of sequences to sample from the alignment")
+	sampleseqCmd.PersistentFlags().Int64VarP(&sampleseqSeed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
+	sampleseqCmd.PersistentFlags().StringVarP(&sampleseqOutput, "output", "o", "stdout", "Sampled alignment output file")
+}

cmd/samplesites.go

@@ -16,7 +16,7 @@ var sitenb int
 
 // samplesitesCmd represents the samplesites command
 var samplesitesCmd = &cobra.Command{
-	Use:   "samplesites",
+	Use:   "sites",
 	Short: "Take a random subalignment",
 	Long: `Take a random subalignment.
 
@@ -48,7 +48,7 @@ and with a given length.
 }
 
 func init() {
-	RootCmd.AddCommand(samplesitesCmd)
+	sampleCmd.AddCommand(samplesitesCmd)
 	samplesitesCmd.PersistentFlags().Int64VarP(&siteseed, "seed", "s", time.Now().UTC().UnixNano(), "Initial Random Seed")
 	samplesitesCmd.PersistentFlags().StringVarP(&siteout, "output", "o", "stdout", "Alignment output file")
 	samplesitesCmd.PersistentFlags().IntVarP(&sitelength, "length", "l", 10, "Length of the random sub alignment")