| 1 | #!/bin/bash |
|---|
| 2 | source tests/test_helper.sh |
|---|
| 3 | |
|---|
| 4 | TEST_ARB=$TEST_ARGS |
|---|
| 5 | maketmpdir T |
|---|
| 6 | |
|---|
| 7 | cp $TEST_ARB $T/ref.arb |
|---|
| 8 | |
|---|
| 9 | SINA="./src/sina $SINA_EXTRA_PARAMS" |
|---|
| 10 | |
|---|
| 11 | SINA="$SINA -i $T/ref.arb --db $T/ref.arb --orig-db $T/ref.arb -o /dev/null --show-dist" |
|---|
| 12 | SINA="$SINA --threads 10 --fs-engine internal" |
|---|
| 13 | |
|---|
| 14 | begin_test "prealigned" |
|---|
| 15 | capture_stdouterr "$SINA --select-step 250 --prealigned" |
|---|
| 16 | assert_exit_success |
|---|
| 17 | assert_output_contains "align 48 sequences" |
|---|
| 18 | assert_output_contains "avg_sps: 1" |
|---|
| 19 | assert_output_contains "avg_cpm: 0" |
|---|
| 20 | assert_output_contains "avg_idty: 0" |
|---|
| 21 | end_test |
|---|
| 22 | |
|---|
| 23 | |
|---|
| 24 | begin_test "align copy" |
|---|
| 25 | capture_stdouterr "$SINA --select-step 1000" |
|---|
| 26 | assert_exit_success |
|---|
| 27 | assert_output_contains "align 12 sequences" |
|---|
| 28 | assert_output_contains "avg_sps: 1" |
|---|
| 29 | assert_output_contains "avg_cpm: 0" |
|---|
| 30 | assert_output_contains "avg_idty: 1" |
|---|
| 31 | end_test |
|---|
| 32 | |
|---|
| 33 | begin_test "realign" |
|---|
| 34 | capture_stdouterr "$SINA --select-step 250 --realign" |
|---|
| 35 | assert_exit_success |
|---|
| 36 | assert_output_contains "align 48 sequences" |
|---|
| 37 | assert_output_value avg_sps: ">0.996" |
|---|
| 38 | assert_output_value avg_cpm: "<0.0002" |
|---|
| 39 | assert_output_value avg_idty: ">0.96" |
|---|
| 40 | end_test |
|---|
| 41 | |
|---|
| 42 | begin_test "realign/noquery" |
|---|
| 43 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out" |
|---|
| 44 | assert_exit_success |
|---|
| 45 | assert_output_contains "align 48 sequences" |
|---|
| 46 | assert_output_value avg_sps: ">0.996" |
|---|
| 47 | assert_output_value avg_cpm: "<0.00025" |
|---|
| 48 | assert_output_value avg_idty: ">0.96" |
|---|
| 49 | end_test |
|---|
| 50 | |
|---|
| 51 | begin_test "realign/noquery k=8" |
|---|
| 52 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-kmer-len 8" |
|---|
| 53 | assert_exit_success |
|---|
| 54 | assert_output_contains "align 48 sequences" |
|---|
| 55 | assert_output_value avg_sps: ">0.996" |
|---|
| 56 | assert_output_value avg_cpm: "<0.0002" |
|---|
| 57 | assert_output_value avg_idty: ">0.96" |
|---|
| 58 | end_test |
|---|
| 59 | |
|---|
| 60 | begin_test "realign/noquery nofast" |
|---|
| 61 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-kmer-no-fast" |
|---|
| 62 | assert_exit_success |
|---|
| 63 | assert_output_contains "align 48 sequences" |
|---|
| 64 | assert_output_value avg_sps: ">0.996" |
|---|
| 65 | assert_output_value avg_cpm: "<0.00015" |
|---|
| 66 | assert_output_value avg_idty: ">0.96" |
|---|
| 67 | end_test |
|---|
| 68 | |
|---|
| 69 | begin_test "realign msc 0.9" |
|---|
| 70 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.9" |
|---|
| 71 | assert_exit_success |
|---|
| 72 | assert_output_contains "align 48 sequences" |
|---|
| 73 | assert_output_value avg_sps: ">0.99" |
|---|
| 74 | assert_output_value avg_cpm: "<0.001" |
|---|
| 75 | assert_output_value avg_idty: ">0.88" "<0.9" |
|---|
| 76 | end_test |
|---|
| 77 | |
|---|
| 78 | begin_test "realign msc 0.8" |
|---|
| 79 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.8" |
|---|
| 80 | assert_exit_success |
|---|
| 81 | assert_output_contains "align 48 sequences" |
|---|
| 82 | assert_output_value avg_sps: ">0.97" |
|---|
| 83 | assert_output_value avg_cpm: "<0.002" |
|---|
| 84 | assert_output_value avg_idty: ">0.78" "<0.8" |
|---|
| 85 | end_test |
|---|
| 86 | |
|---|
| 87 | begin_test "realign msc 0.7" |
|---|
| 88 | capture_stdouterr "$SINA --select-step 250 --realign --fs-leave-query-out --fs-msc-max 0.7" |
|---|
| 89 | assert_exit_success |
|---|
| 90 | assert_output_contains "align 48 sequences" |
|---|
| 91 | assert_output_value avg_sps: ">0.95" |
|---|
| 92 | assert_output_value avg_cpm: "<0.01" |
|---|
| 93 | assert_output_value avg_idty: ">0.68" "<0.7" |
|---|
| 94 | end_test |
|---|
| 95 | |
|---|
| 96 | |
|---|
| 97 | |
|---|
