Added invertebrate mitochondrial code

align/align_test.go

@@ -1045,6 +1045,49 @@ func TestTranslateMito(t *testing.T) {
 	}
 }
 
+func TestTranslateMitoI(t *testing.T) {
+
+	in := NewSeqBag(UNKNOWN)
+	in.AddSequence("Seq0000", "ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTAGTGTAATGATAGC", "")
+	in.AddSequence("Seq0001", "ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA", "")
+	in.AutoAlphabet()
+
+	in2, err2 := in.CloneSeqBag()
+	if err2 != nil {
+		t.Error(err2)
+	}
+
+	expaa := NewSeqBag(UNKNOWN)
+	expaa.AddSequence("Seq0000", "MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIMVVVV*W*", "")
+	expaa.AddSequence("Seq0001", "MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIMVVV*W", "")
+	expaa.AutoAlphabet()
+
+	exp3phases := NewSeqBag(UNKNOWN)
+	exp3phases.AddSequence("Seq0000_0", "MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIMVVVV*W*", "")
+	exp3phases.AddSequence("Seq0000_1", "WMTFSVALPHRNSLPHRVAKSLPQRVAEGGITITLS*LS*CNDS", "")
+	exp3phases.AddSequence("Seq0000_2", "GWLFLLPSPTATVFLIE*RSDYHNGWRSVASLLHYHSCRSVMM", "")
+	exp3phases.AddSequence("Seq0001_0", "MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIMVVV*W", "")
+	exp3phases.AddSequence("Seq0001_1", "WMTFSVALPHRNSLPHRVAKSLPQRVAEGGITITLS*LSYN", "")
+	exp3phases.AddSequence("Seq0001_2", "GWLFLLPSPTATVFLIE*RSDYHNGWRSVASLLHYHSCRMM", "")
+	exp3phases.AutoAlphabet()
+
+	if err := in.Translate(0, 2); err != nil {
+		t.Error(err)
+	} else {
+		if !expaa.Identical(in) {
+			t.Error(fmt.Errorf("Expected sequences are different from phased sequences"))
+		}
+	}
+
+	if err := in2.Translate(-1, 2); err != nil {
+		t.Error(err)
+	} else {
+		if !exp3phases.Identical(in2) {
+			t.Error(fmt.Errorf("Expected sequences are different from 3 phase translated sequences"))
+		}
+	}
+}
+
 func TestMaskNt(t *testing.T) {
 	in := NewAlign(UNKNOWN)
 	in.AddSequence("Seq0000", "GATTAATTTGCCGTAGGCCA", "")

align/const.go

@@ -31,8 +31,9 @@ const (
 	POSITION_SEMI_CONSERVED = 2 // Same weak group
 	POSITION_NOT_CONSERVED  = 3 // None of the above values
 
-	GENETIC_CODE_STANDARD       = 0 // Standard genetic code
-	GENETIC_CODE_VETEBRATE_MITO = 1 // Vertebrate mitochondrial genetic code
+	GENETIC_CODE_STANDARD         = 0 // Standard genetic code
+	GENETIC_CODE_VETEBRATE_MITO   = 1 // Vertebrate mitochondrial genetic code
+	GENETIC_CODE_INVETEBRATE_MITO = 2 // Invertebrate mitochondrial genetic code
 )
 
 var stdaminoacid = []rune{'A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V'}
@@ -88,12 +89,39 @@ var vertebratemitocode = map[string]rune{
 	"AGA": '*', "AGG": '*', "TAA": '*', "TAG": '*',
 }
 
+var invertebratemitocode = map[string]rune{
+	"---": '-',
+	"GCT": 'A', "GCC": 'A', "GCA": 'A', "GCG": 'A',
+	"TTA": 'L', "TTG": 'L', "CTT": 'L', "CTC": 'L', "CTA": 'L', "CTG": 'L',
+	"CGT": 'R', "CGC": 'R', "CGA": 'R', "CGG": 'R',
+	"AAA": 'K', "AAG": 'K',
+	"AAT": 'N', "AAC": 'N',
+	"ATG": 'M', "ATA": 'M',
+	"GAT": 'D', "GAC": 'D',
+	"TTT": 'F', "TTC": 'F',
+	"TGT": 'C', "TGC": 'C',
+	"CCT": 'P', "CCC": 'P', "CCA": 'P', "CCG": 'P',
+	"CAA": 'Q', "CAG": 'Q',
+	"AGA": 'S', "AGG": 'S', "TCT": 'S', "TCC": 'S', "TCA": 'S', "TCG": 'S', "AGT": 'S', "AGC": 'S',
+	"GAA": 'E', "GAG": 'E',
+	"ACT": 'T', "ACC": 'T', "ACA": 'T', "ACG": 'T',
+	"GGT": 'G', "GGC": 'G', "GGA": 'G', "GGG": 'G',
+	"TGG": 'W', "TGA": 'W',
+	"CAT": 'H', "CAC": 'H',
+	"TAT": 'Y', "TAC": 'Y',
+	"ATT": 'I', "ATC": 'I',
+	"GTT": 'V', "GTC": 'V', "GTA": 'V', "GTG": 'V',
+	"TAA": '*', "TAG": '*',
+}
+
 func geneticCode(code int) (gencode map[string]rune, err error) {
 	switch code {
 	case GENETIC_CODE_STANDARD:
 		gencode = standardcode
 	case GENETIC_CODE_VETEBRATE_MITO:
 		gencode = vertebratemitocode
+	case GENETIC_CODE_INVETEBRATE_MITO:
+		gencode = invertebratemitocode
 	default:
 		err = fmt.Errorf("This genetic code does not exis")
 	}

cmd/phase.go

@@ -116,6 +116,8 @@ Output file is an unaligned set of sequences in fasta.
 			geneticcode = align.GENETIC_CODE_STANDARD
 		case "mitov":
 			geneticcode = align.GENETIC_CODE_VETEBRATE_MITO
+		case "mitoi":
+			geneticcode = align.GENETIC_CODE_INVETEBRATE_MITO
 		default:
 			err = fmt.Errorf("Unknown genetic code : %s", phaseGeneticCode)
 			return
@@ -172,7 +174,7 @@ Output file is an unaligned set of sequences in fasta.
 func init() {
 	RootCmd.AddCommand(phaseCmd)
 	phaseCmd.PersistentFlags().StringVarP(&phaseOutput, "output", "o", "stdout", "Output \"phased\" FASTA file")
-	phaseCmd.PersistentFlags().StringVar(&phaseGeneticCode, "genetic-code", "standard", "Genetic Code: standard, or mitov (vertebrate mitochondrial)")
+	phaseCmd.PersistentFlags().StringVar(&phaseGeneticCode, "genetic-code", "standard", "Genetic Code: standard, mitoi (invertebrate mitochondrial) or mitov (vertebrate mitochondrial)")
 	phaseCmd.PersistentFlags().StringVar(&phaseAAOutput, "aa-output", "none", "Output Met \"phased\" aa FASTA file")
 	phaseCmd.PersistentFlags().StringVarP(&phaseLogOutput, "log", "l", "none", "Output log: positions of the considered Start for each sequence")
 	phaseCmd.PersistentFlags().Float64Var(&lencutoff, "len-cutoff", -1.0, "Length cutoff, over orf length, to consider sequence hits (-1==No cutoff)")

cmd/phasent.go

@@ -120,6 +120,8 @@ Output file is an unaligned set of sequences in fasta.
 			geneticcode = align.GENETIC_CODE_STANDARD
 		case "mitov":
 			geneticcode = align.GENETIC_CODE_VETEBRATE_MITO
+		case "mitoi":
+			geneticcode = align.GENETIC_CODE_INVETEBRATE_MITO
 		default:
 			err = fmt.Errorf("Unknown genetic code : %s", phaseGeneticCode)
 			return
@@ -196,7 +198,7 @@ func init() {
 	RootCmd.AddCommand(phasentCmd)
 	phasentCmd.PersistentFlags().StringVarP(&phaseOutput, "output", "o", "stdout", "Output ATG \"phased\" FASTA file")
 	phasentCmd.PersistentFlags().StringVar(&phaseCodonOutput, "nt-output", "none", "Output ATG \"phased\" FASTA file + first nts not in ref phase removed (nt corresponding to aa-output sequence)")
-	phasentCmd.PersistentFlags().StringVar(&phaseGeneticCode, "genetic-code", "standard", "Genetic Code: standard, or mitov (vertebrate mitochondrial)")
+	phasentCmd.PersistentFlags().StringVar(&phaseGeneticCode, "genetic-code", "standard", "Genetic Code: standard, mitoi (invertebrate mitochondrial) or mitov (vertebrate mitochondrial)")
 	phasentCmd.PersistentFlags().StringVar(&phaseAAOutput, "aa-output", "none", "Output translated sequences FASTA file")
 	phasentCmd.PersistentFlags().StringVarP(&phaseLogOutput, "log", "l", "none", "Output log: positions of the considered ATG for each sequence")
 	phasentCmd.PersistentFlags().Float64Var(&lencutoff, "len-cutoff", -1.0, "Length cutoff, over orf length, to consider sequence hits (-1==No cutoff)")

cmd/translate.go

@@ -47,6 +47,9 @@ It only translates using the standard genetic code so far.
 			geneticcode = align.GENETIC_CODE_STANDARD
 		case "mitov":
 			geneticcode = align.GENETIC_CODE_VETEBRATE_MITO
+		case "mitoi":
+			geneticcode = align.GENETIC_CODE_INVETEBRATE_MITO
+
 		default:
 			err = fmt.Errorf("Unknown genetic code : %s", translateGeneticCode)
 			return
@@ -92,7 +95,7 @@ It only translates using the standard genetic code so far.
 
 func init() {
 	RootCmd.AddCommand(translateCmd)
-	translateCmd.PersistentFlags().StringVar(&translateGeneticCode, "genetic-code", "standard", "Genetic Code: standard, or mitov (vertebrate mitochondrial)")
+	translateCmd.PersistentFlags().StringVar(&translateGeneticCode, "genetic-code", "standard", "Genetic Code: standard, mitoi (invertebrate mitochondrial) or mitov (vertebrate mitochondrial)")
 	translateCmd.PersistentFlags().StringVarP(&translateOutput, "output", "o", "stdout", "Output translated alignment file")
 	translateCmd.PersistentFlags().IntVar(&translatePhase, "phase", 0, "Number of characters to drop from the start of the alignment (if -1: Translate in the 3 phases, from positions 0, 1, and 2)")
 	translateCmd.PersistentFlags().BoolVar(&unaligned, "unaligned", false, "Considers sequences as unaligned and format fasta (phylip, nexus,... options are ignored)")

test.sh

@@ -1926,7 +1926,7 @@ ${GOALIGN} translate -i input --phase 0 --unaligned -o result
 diff -q -b expected result
 rm -f input expected result
 
-echo "->goalign translate 3 phases"
+echo "->goalign translate 3 phases (standard)"
 cat > input <<EOF
 >test1 
 CATGAGTCTCTCTGATAAGGACAAGGCTGCTGTGAAAGCCCTATGG 
@@ -1968,6 +1968,31 @@ ${GOALIGN} translate -i input --phase -1 --unaligned --genetic-code mitov -o res
 diff -q -b expected result
 rm -f input expected result
 
+echo "->goalign translate 3 phases (mito invertebrate)"
+cat > input <<EOF
+>s1
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTAGTGTAATGATAGC
+>s2
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA
+EOF
+cat > expected <<EOF
+>s1_0
+MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIMVVVV*W*
+>s1_1
+WMTFSVALPHRNSLPHRVAK*LPQRVAEGGITITLS*LS*CNDS
+>s1_2
+GWLFLLPSPTATVFLIE*R*DYHNGWR*VASLLHYHSCRSVMM
+>s2_0
+MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIMVVV*W
+>s2_1
+WMTFSVALPHRNSLPHRVAK*LPQRVAEGGITITLS*LSYN
+>s2_2
+GWLFLLPSPTATVFLIE*R*DYHNGWR*VASLLHYHSCRMM
+EOF
+${GOALIGN} translate -i input --phase -1 --unaligned --genetic-code mitov -o result
+diff -q -b expected result
+rm -f input expected result
+
 echo "->goalign dedup"
 cat > input <<EOF
   5   6