Modified tests

test.sh

@@ -2066,6 +2066,40 @@ diff expected result
 diff expected.aa result.aa
 rm -f input expected result expected.aa result.aa
 
+echo "->goalign phasent"
+cat > input <<EOF
+>allcodons
+GCTGCCGCAGCGTTATTGCTTCTCCTACTGCGTCGCCGACGGAGAAGGAAAAAGAATAACATG
+GATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACT
+ACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTAGTGTAATGA
+TAGC
+>allcodons2
+GCTGCAGCGTTATTGCTTCTCCTACTGCGTCGCCGACGGAGAAGGAAAAAGAATAACATG
+GATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACT
+ACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA
+EOF
+cat > expected <<EOF
+>allcodons
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
+CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTAGTGTAATGATAGC
+>allcodons2
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
+CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA
+EOF
+
+cat > expected.aa <<EOF
+>allcodons
+MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIIVVVV***
+>allcodons2
+MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIIVVV**
+EOF
+
+goalign phasent -i input --unaligned -o result --aa-output result.aa
+diff expected result
+diff expected.aa result.aa
+rm -f input expected result expected.aa result.aa
+
+
 echo "->goalign phase reverse"
 cat > input <<EOF
 >allcodons
@@ -2087,6 +2121,35 @@ ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
 CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA
 EOF
 
+goalign phase -i input --unaligned -o result  --reverse
+diff expected result
+rm -f input expected result
+
+echo "->goalign phasent reverse"
+cat > input <<EOF
+>allcodons
+GCTATCATTACACTACGACAACTATGATAATGTAATAGTGATGCCACCCTCCGCCACCCG
+TTGTGGTAGTCTCTTCGCTACTCGATGAGGAAGACTGTTGCGGTGGGGGAGGGCAACAGA
+AAAAGTCATCCATGTTATTCTTTTTCCTTCTCCGTCGGCGACGCAGTAGGAGAAGCAATA
+ACGCTGCGGCAGC
+>allcodons2
+GCTGCAGCGTTATTGCTTCTCCTACTGCGTCGCCGACGGAGAAGGAAAAAGAATAACATG
+GATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACT
+ACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA
+EOF
+cat > expected <<EOF
+>allcodons
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
+CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTAGTGTAATGATAGC
+>allcodons2
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
+CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA
+EOF
+goalign phasent -i input --unaligned -o result  --reverse
+diff expected result
+rm -f input expected result
+
+
 echo "->goalign phase reverse cutends"
 cat > input <<EOF
 >allcodons
@@ -2108,7 +2171,6 @@ ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
 CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTA
 EOF
 
-
 cat > expected.aa <<EOF
 >allcodons
 MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIIVVVV*
@@ -2121,6 +2183,39 @@ diff expected result
 diff expected.aa result.aa
 rm -f input expected result expected.aa result.aa
 
+echo "->goalign phasent reverse cutends"
+cat > input <<EOF
+>allcodons
+GCTATCATTACACTACGACAACTATGATAATGTAATAGTGATGCCACCCTCCGCCACCCG
+TTGTGGTAGTCTCTTCGCTACTCGATGAGGAAGACTGTTGCGGTGGGGGAGGGCAACAGA
+AAAAGTCATCCATGTTATTCTTTTTCCTTCTCCGTCGGCGACGCAGTAGGAGAAGCAATA
+ACGCTGCGGCAGC
+>allcodons2
+GCTGCAGCGTTATTGCTTCTCCTACTGCGTCGCCGACGGAGAAGGAAAAAGAATAACATG
+GATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACT
+ACCACAACGGGTGGCGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAATGA
+EOF
+cat > expected <<EOF
+>allcodons
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
+CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTAGTGTAA
+>allcodons2
+ATGGATGACTTTTTCTGTTGCCCTCCCCCACCGCAACAGTCTTCCTCATCGAGTAGCGAAGAGACTACCACAACGGGTGG
+CGGAGGGTGGCATCACTATTACATTATCATAGTTGTCGTATAA
+EOF
+
+cat > expected.aa <<EOF
+>allcodons
+MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIIVVVV*
+>allcodons2
+MDDFFCCPPPPQQSSSSSSEETTTTGGGGWHHYYIIIVVV*
+EOF
+
+goalign phasent -i input --unaligned -o result --aa-output result.aa --reverse --cut-end
+diff expected result
+diff expected.aa result.aa
+rm -f input expected result expected.aa result.aa
+
 
 echo "->goalign sw (smith & waterman)"
 cat > input <<EOF