| 1 | #!/bin/bash |
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| 2 | source tests/test_helper.sh |
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| 3 | |
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| 4 | TEST_ARB=$TEST_ARGS |
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| 5 | maketmpdir T |
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| 6 | |
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| 7 | cp $TEST_ARB $T/ref.arb |
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| 8 | |
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| 9 | SINA="./src/sina" |
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| 10 | |
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| 11 | begin_test "PREP" |
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| 12 | capture_stdouterr "$SINA -i $T/ref.arb -o $T/extracted.fasta --select-step 1000 --prealigned" |
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| 13 | assert_exit_success |
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| 14 | assert_output_contains "align 12 sequences" |
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| 15 | capture_stdouterr "$SINA -i $T/ref.arb -o $T/extracted.arb --select-step 1000 --prealigned" |
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| 16 | assert_exit_success |
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| 17 | assert_output_contains "align 12 sequences" |
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| 18 | end_test |
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| 19 | |
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| 20 | begin_test "Align from FASTA->FASTA" |
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| 21 | capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.fasta --preserve-order --realign --db $T/extracted.arb" |
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| 22 | assert_output_contains "align 12 sequences" |
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| 23 | assert_exit_success |
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| 24 | end_test |
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| 25 | |
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| 26 | begin_test "Align from FASTA->FASTA(stdout)" |
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| 27 | capture_stdouterr "$SINA -i $T/extracted.fasta --preserve-order --realign --db $T/extracted.arb >$T/aligned.2.fasta" |
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| 28 | assert_output_contains "align 12 sequences" |
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| 29 | assert_exit_success |
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| 30 | capture_stdouterr "cmp $T/aligned.fasta $T/aligned.2.fasta" |
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| 31 | assert_exit_success |
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| 32 | end_test |
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| 33 | |
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| 34 | begin_test "Align from FASTA->ARB" |
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| 35 | capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.arb --realign --db $T/extracted.arb" |
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| 36 | assert_output_contains "align 12 sequences" |
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| 37 | assert_exit_success |
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| 38 | end_test |
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| 39 | |
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| 40 | begin_test "Align from ARB->ARB" |
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| 41 | capture_stdouterr "$SINA -i $T/extracted.arb -o $T/aligned.arb --realign --db $T/extracted.arb" |
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| 42 | assert_output_contains "align 12 sequences" |
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| 43 | assert_exit_success |
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| 44 | end_test |
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| 45 | |
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| 46 | begin_test "Add relatives FASTA->FASTA" |
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| 47 | capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.fasta --add-relatives 2 --db $T/ref.arb -v" |
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| 48 | assert_output_contains "align 12 sequences" |
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| 49 | assert_output_contains "wrote 36 sequences (0 excluded, 24 relatives)" |
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| 50 | end_test |
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| 51 | |
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| 52 | begin_test "Add relatives FASTA->ARB" |
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| 53 | capture_stdouterr "$SINA -i $T/extracted.fasta -o $T/aligned.arb --add-relatives 2 --db $T/ref.arb -v" |
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| 54 | assert_output_contains "align 12 sequences" |
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| 55 | assert_output_contains "wrote 36 sequences (0 excluded, 24 relatives)" |
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| 56 | end_test |
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| 57 | |
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