| 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 $T/ref.arb |
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| 8 | |
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| 9 | SINA="./src/sina" |
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| 10 | |
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| 11 | SINA="$SINA -i $T/ref.arb --db $T/ref.arb --orig-db $T/ref.arb -o /dev/null --show-dist" |
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| 12 | SINA="$SINA --threads 10 --fs-engine pt-server" |
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| 13 | |
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| 14 | begin_test "prealigned" |
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| 15 | capture_stdouterr "$SINA --select-step 250 --prealigned" |
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| 16 | assert_exit_success |
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| 17 | assert_output_contains "align 48 sequences" |
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| 18 | assert_output_contains "avg_sps: 1" |
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| 19 | assert_output_contains "avg_cpm: 0" |
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| 20 | assert_output_contains "avg_idty: 0" |
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| 21 | end_test |
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| 22 | |
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| 23 | |
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| 24 | begin_test "align copy" |
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| 25 | capture_stdouterr "$SINA --select-step 1000" |
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| 26 | assert_exit_success |
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| 27 | assert_output_contains "align 12 sequences" |
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| 28 | assert_output_contains "avg_sps: 1" |
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| 29 | assert_output_contains "avg_cpm: 0" |
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| 30 | assert_output_contains "avg_idty: 1" |
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| 31 | end_test |
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| 32 | |
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| 33 | begin_test "realign" |
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| 34 | capture_stdouterr "$SINA --select-step 250 --realign" |
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| 35 | assert_exit_success |
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| 36 | assert_output_contains "align 48 sequences" |
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| 37 | assert_output_value avg_sps: ">0.996" |
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| 38 | assert_output_value avg_cpm: "<0.0002" |
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| 39 | assert_output_value avg_idty: ">0.96" |
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| 40 | end_test |
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| 41 | |
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| 42 | begin_test "realign/noquery" |
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| 43 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out" |
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| 44 | assert_exit_success |
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| 45 | assert_output_contains "align 48 sequences" |
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| 46 | assert_output_value avg_sps: ">0.996" |
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| 47 | assert_output_value avg_cpm: "<0.00025" |
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| 48 | assert_output_value avg_idty: ">0.96" |
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| 49 | end_test |
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| 50 | |
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| 51 | begin_test "realign/noquery k=8" |
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| 52 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-kmer-len 8" |
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| 53 | assert_exit_success |
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| 54 | assert_output_contains "align 48 sequences" |
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| 55 | assert_output_value avg_sps: ">0.996" |
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| 56 | assert_output_value avg_cpm: "<0.0002" |
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| 57 | assert_output_value avg_idty: ">0.96" |
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| 58 | end_test |
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| 59 | |
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| 60 | begin_test "realign/noquery nofast" |
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| 61 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-kmer-no-fast" |
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| 62 | assert_exit_success |
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| 63 | assert_output_contains "align 48 sequences" |
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| 64 | assert_output_value avg_sps: ">0.996" |
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| 65 | assert_output_value avg_cpm: "<0.00015" |
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| 66 | assert_output_value avg_idty: ">0.96" |
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| 67 | end_test |
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| 68 | |
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| 69 | |
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| 70 | begin_test "realign msc 0.9" |
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| 71 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.9" |
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| 72 | assert_exit_success |
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| 73 | assert_output_contains "align 48 sequences" |
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| 74 | assert_output_value avg_sps: ">0.99" |
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| 75 | assert_output_value avg_cpm: "<0.001" |
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| 76 | assert_output_value avg_idty: ">0.88" "<0.9" |
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| 77 | end_test |
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| 78 | |
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| 79 | begin_test "realign msc 0.8" |
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| 80 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.8" |
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| 81 | assert_exit_success |
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| 82 | assert_output_contains "align 48 sequences" |
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| 83 | assert_output_value avg_sps: ">0.97" |
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| 84 | assert_output_value avg_cpm: "<0.002" |
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| 85 | assert_output_value avg_idty: ">0.78" "<0.8" |
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| 86 | end_test |
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| 87 | |
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| 88 | begin_test "realign msc 0.7" |
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| 89 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.7" |
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| 90 | assert_exit_success |
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| 91 | assert_output_contains "align 48 sequences" |
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| 92 | assert_output_value avg_sps: ">0.95" |
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| 93 | assert_output_value avg_cpm: "<0.01" |
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| 94 | assert_output_value avg_idty: ">0.68" "<0.7" |
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| 95 | end_test |
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