Added --reverse option to diff

align/align_test.go

@@ -1336,6 +1336,45 @@ func TestDiffCount(t *testing.T) {
 
 }
 
+func TestDiffReverse(t *testing.T) {
+	in := NewAlign(UNKNOWN)
+	in.AddSequence("Seq0000", "GATTAATTTGCCGTAGGCCAGAATCTGAAGATCGAACACTTTAAGTTTTCACTTCTAATGGAGAGGACTAGTTCATACTTTTTAAACACTTTTACATCGA", "")
+	in.AddSequence("Seq0001", "TG.CGGACCTAA...TTGAGT.CAAC.GT.TATTCCAG.GG.GGAGAGGTCTA.T.TTCC.GTT.A.GG.C.CT.G.GC.G.A..GGGTA.GGC...GTG", "")
+	in.AddSequence("Seq0002", "CTAAGCGCG.G..G.TTG.T.TTGGA.C.AGGTT..ATAC.CGGCAA.G.C.CATG.TCCCCC.A.GAC.A.AAGAG.GAAG.T.GA..AAA.GA.C.CC", "")
+	in.AddSequence("Seq0003", "..G.GGAGGCTTTAT...ACA.GGTATT...GACTGAGGGGC.CCCCGG..TGGTA.GCA.GAGCC.TCGCGAAGGCT.CAGGT.T.TTCC.GTGT.ACC", "")
+	in.AutoAlphabet()
+
+	out, _ := in.Clone()
+	out.ReplaceMatchChars()
+
+	i := 0
+	var ref []rune
+	out.IterateChar(func(name string, seq []rune) {
+		orig, _ := in.GetSequenceCharById(i)
+		if i == 0 {
+			ref = seq
+			for site := 0; site < out.Length(); site++ {
+				if seq[site] != orig[site] {
+					t.Errorf("Original reference character has been changed (%c vs. %c)", orig[site], seq[site])
+				}
+			}
+		} else {
+			for site := 0; site < out.Length(); site++ {
+				if orig[site] == POINT {
+					if seq[site] != ref[site] {
+						t.Errorf(". has not been replaced by the right character (%c vs. %c)", ref[site], seq[site])
+					}
+				} else {
+					if seq[site] != orig[site] {
+						t.Errorf("Original character has been changed (%c vs. %c)", orig[site], seq[site])
+					}
+				}
+			}
+		}
+		i++
+	})
+}
+
 func TestCompress(t *testing.T) {
 	in := NewAlign(UNKNOWN)
 	in.AddSequence("Seq0000", "GGTTTTTTTT", "")

cmd/diff.go

@@ -14,6 +14,7 @@ import (
 var diffOutput string
 var diffCount bool
 var diffNoGaps bool
+var reverse bool
 
 // statsCmd represents the stats command
 var diffCmd = &cobra.Command{
@@ -31,6 +32,8 @@ The format is tab separated, with following columns:
 1. Sequence name (reference sequence is not included)
 2,...,end: For each type of change, its number of occurence
 
+
+If option --reverse is given, then replaces . with the characters on the first sequence
 `,
 	RunE: func(cmd *cobra.Command, args []string) (err error) {
 		var aligns *align.AlignChannel
@@ -52,7 +55,11 @@ The format is tab separated, with following columns:
 				alldiffs, diffs := al.CountDifferences()
 				writeDiffCounts(al, alldiffs, diffs, f)
 			} else {
-				al.DiffWithFirst()
+				if reverse {
+					al.ReplaceMatchChars()
+				} else {
+					al.DiffWithFirst()
+				}
 				writeAlign(al, f)
 			}
 		}
@@ -90,5 +97,6 @@ func init() {
 	diffCmd.PersistentFlags().StringVarP(&diffOutput, "output", "o", "stdout", "Diff output file")
 	diffCmd.PersistentFlags().BoolVar(&diffCount, "counts", false, "Count differences instead of writting only identical characters")
 	diffCmd.PersistentFlags().BoolVar(&diffNoGaps, "no-gaps", false, "Do not count gaps (only with --counts)")
+	diffCmd.PersistentFlags().BoolVar(&reverse, "reverse", false, "Restore identical characters (.) using first sequence positions")
 	RootCmd.AddCommand(diffCmd)
 }

test.sh

@@ -3019,6 +3019,78 @@ ${GOALIGN} diff -i input -p --one-line -o result --counts
 diff -q -b  expected result
 rm -f input expected result
 
+echo "->goalign diff --reverse"
+
+cat > input <<EOF
+>Seq0000
+GATTAATTTGCCGTAGGCCAGAATCTGAAGATCGAACACTTTAAGTTTTCACTTCTAATGGAGAGGACTAGTTCATACTT
+TTTAAACACTTTTACATCGA
+>Seq0001
+TG.CGGACCTAA...TTGAGT.CAAC.GT.TATTCCAG.GG.GGAGAGGTCTA.T.TTCC.GTT.A.GG.C.CT.G.GC.
+G.A..GGGTA.GGC...GTG
+>Seq0002
+CTAAGCGCG.G..G.TTG.T.TTGGA.C.AGGTT..ATAC.CGGCAA.G.C.CATG.TCCCCC.A.GAC.A.AAGAG.GA
+AG.T.GA..AAA.GA.C.CC
+>Seq0003
+..G.GGAGGCTTTAT...ACA.GGTATT...GACTGAGGGGC.CCCCGG..TGGTA.GCA.GAGCC.TCGCGAAGGCT.C
+AGGT.T.TTCC.GTGT.ACC
+>Seq0004
+C..AGCCCCTGATGCCCTG.CCCGTGTCGCGG.A.CGT..AC.TT.CACG.TAAA..C.CCGCT.CTAGTCGG.TCTAGA
+.GCTTTTCT.CCAGATCT.G
+>Seq0005
+AG..TGAC.ATGAGC.C.GGCTTAG..CT..CA.TGATGC.CCGT.G.AAGGG..CTGAT.TTCTTGTGCTCG.GC.TA.
+.AG.GCTGAG...C.CAAAG
+>Seq0006
+TCGCC.CGGTGT.G.ATGT.CGT.A..GCAG.AATCAG.GGCTTTCACCG..A.GCCCCCTCCGT.G..CC..GCG..CA
+.CGGCGG..C.GCGGTGTCG
+>Seq0007
+CTGGT.A.AC.T.CGCTATTTCG..A.TTCG.GT.CGGG.AACGA.AGCGGT.AA.GC.TATTCC..TC..C...C..CC
+A.G..GGTGGC.CTGGAGCC
+>Seq0008
+TCG.T.ACCCA.TCTAA...CCTC...T..CGAC.T.GGG.GCTCGGC.TGGA.ACCT.C.TC.TATTGGACC.CAGG.C
+.CA.CCTCG.GAGCTC..TG
+>Seq0009
+ACC..CGGCT.TAG.CAG.T...GTCCGGTTC...G....G..C.GAAA.TTGAAA.GGCTC..C.GAGGC..GT.C.GC
+AGAGTGGGAC.A..ACATAC
+EOF
+
+cat > expected <<EOF
+>Seq0000
+GATTAATTTGCCGTAGGCCAGAATCTGAAGATCGAACACTTTAAGTTTTCACTTCTAATGGAGAGGACTAGTTCATACTT
+TTTAAACACTTTTACATCGA
+>Seq0001
+TGTCGGACCTAAGTATTGAGTACAACGGTGTATTCCAGCGGTGGAGAGGTCTATTTTTCCGGTTGAAGGACTCTAGAGCT
+GTAAAGGGTATGGCCATGTG
+>Seq0002
+CTAAGCGCGGGCGGATTGCTGTTGGAGCAAGGTTAAATACTCGGCAATGCCCCATGATCCCCCAAGGACAATAAGAGCGA
+AGTTAGAACAAATGAACCCC
+>Seq0003
+GAGTGGAGGCTTTATGGCACAAGGTATTAGAGACTGAGGGGCACCCCGGCATGGTAAGCAGGAGCCATCGCGAAGGCTTC
+AGGTATCTTCCTGTGTTACC
+>Seq0004
+CATAGCCCCTGATGCCCTGACCCGTGTCGCGGCAACGTCTACATTTCACGATAAATACTCCGCTGCTAGTCGGCTCTAGA
+TGCTTTTCTTCCAGATCTGG
+>Seq0005
+AGTTTGACTATGAGCGCCGGCTTAGTGCTGACAGTGATGCTCCGTTGTAAGGGTCCTGATGTTCTTGTGCTCGCGCATAT
+TAGAGCTGAGTTTCCCAAAG
+>Seq0006
+TCGCCACGGTGTGGAATGTACGTTATGGCAGTAATCAGCGGCTTTCACCGACATGCCCCCTCCGTGGCTCCTTGCGACCA
+TCGGCGGACCTGCGGTGTCG
+>Seq0007
+CTGGTAATACCTGCGCTATTTCGTCAGTTCGTGTACGGGTAACGATAGCGGTTAATGCTTATTCCGATCAGCTCACACCC
+ATGAAGGTGGCTCTGGAGCC
+>Seq0008
+TCGTTAACCCACTCTAACCACCTCCTGTAGCGACATCGGGTGCTCGGCTTGGATACCTTCGTCATATTGGACCCCAGGTC
+TCAACCTCGTGAGCTCTCTG
+>Seq0009
+ACCTACGGCTCTAGACAGCTGAAGTCCGGTTCCGAGCACTGTACGGAAACTTGAAAAGGCTCGACGGAGGCTTGTTCCGC
+AGAGTGGGACTATAACATAC
+EOF
+
+${GOALIGN} diff --reverse -i input -o result
+diff -q -b  expected result
+rm -f input expected result
+
 
 echo "->goalign stats auto from 1000 random phylip alignments"
 cat > expected.nb <<EOF