Addded --nb-samples option to sample seqs

cmd/sampleseq.go

@@ -9,7 +9,8 @@ import (
 )
 
 var sampleseqOutput string
-var sampleseqNb int
+var sampleseqSize int
+var sampleseqNbSamples int
 
 // sampleCmd represents the sample command
 var sampleseqCmd = &cobra.Command{
@@ -21,7 +22,15 @@ 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
+As output, writes an alignment containing a sample of the sequences.
+
+All alignments are written on the output in the following order:
+For each input alignment
+  For each sample
+    write(sampled alignment)
+
+It is advised to manipulate phylip alignments, in order to be able to
+divide the output file with 'goalign divide' for example.
 
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
@@ -40,24 +49,28 @@ As output, writes an alignment containing a sample of the sequences
 		defer closeWriteFile(f, sampleseqOutput)
 
 		for al := range aligns.Achan {
-			if sample, err = al.Sample(sampleseqNb); err != nil {
-				io.LogError(err)
-				return
-			} else {
-				writeAlign(sample, f)
+			for i := 0; i < sampleseqNbSamples; i++ {
+				if sample, err = al.Sample(sampleseqSize); err != nil {
+					io.LogError(err)
+					return
+				} else {
+					writeAlign(sample, f)
+				}
 			}
 		}
 
 		if aligns.Err != nil {
 			err = aligns.Err
 			io.LogError(err)
 		}
+
 		return
 	},
 }
 
 func init() {
 	sampleCmd.AddCommand(sampleseqCmd)
-	sampleseqCmd.PersistentFlags().IntVarP(&sampleseqNb, "nb-seq", "n", 1, "Number of sequences to sample from the alignment")
+	sampleseqCmd.PersistentFlags().IntVarP(&sampleseqSize, "nb-seq", "n", 1, "Number of sequences to sample from the alignment")
+	sampleseqCmd.PersistentFlags().IntVarP(&sampleseqNbSamples, "nb-samples", "s", 1, "Number of samples to generate")
 	sampleseqCmd.PersistentFlags().StringVarP(&sampleseqOutput, "output", "o", "stdout", "Sampled alignment output file")
 }