bea3a22e1454e8fee62a026ffcec8c57af4005be markd Sat Jun 6 13:46:13 2026 -0700 added -tsv option blastToPsl and blastXmlToPsl to allow parsing scores with other programs diff --git src/hg/blastToPsl/tests/expected/protMrnaTsvTest.tsv src/hg/blastToPsl/tests/expected/protMrnaTsvTest.tsv new file mode 100644 index 00000000000..6460dca2d76 --- /dev/null +++ src/hg/blastToPsl/tests/expected/protMrnaTsvTest.tsv @@ -0,0 +1,187 @@ +strand qName qStart qEnd tName tStart tEnd bitScore eVal +++ Q99983 0 421 AB000114 100 1363 773 0 +++ Q99983 194 233 AB001106 3625 3733 22.7 1.1 ++- Q99983 282 305 AB000516 1827 1896 20.4 5.6 +++ Q99983 333 355 AB000449 882 948 20.4 5.6 ++- Q99983 2 19 AB000220 1279 1330 20 7.3 ++- Q99983 157 175 AB001466 551 605 19.6 9.6 +++ Q99984 0 413 AB000115 241 1480 827 0 +++ Q99984 211 228 AB000449 435 486 23.9 0.5 +++ Q99985 0 751 AB000220 562 2815 1547 0 +++ Q99985 340 358 AB000516 1935 1989 21.9 3.6 ++- Q99985 350 377 AB000516 3280 3358 20.8 8.1 ++- Q99985 661 681 AB000468 542 602 21.6 4.8 +++ Q99985 589 605 AB001466 1048 1096 21.6 4.8 ++- Q99985 130 170 AB000462 1762 1882 20.8 8.1 +++ O14490 0 977 AB000277 67 2998 1761 0 ++- O14490 165 224 AB000277 1355 1508 24.6 0.74 ++- O14490 856 866 AB000462 5565 5595 23.9 1.3 +++ O14490 360 390 AB000516 2857 2950 23.5 1.7 +++ Q99986 0 396 AB000449 75 1263 773 0 +++ Q99986 120 137 AB000115 874 925 23.9 0.47 ++- Q99986 98 122 AB001106 3552 3624 20.4 5.2 +++ Q99986 269 291 AB000114 1099 1165 20.4 5.2 +++ P78311 0 1224 AB000459 351 4023 1974 0 +++ P78311 0 1224 AB000460 351 4146 1954 0 +++ P78311 0 789 AB000461 351 2718 1364 0 +++ P78311 801 1224 AB000461 2707 3976 574 0 +++ P78311 146 808 AB001563 708 2694 1130 0 +++ P78311 699 737 AB000277 263 374 26.9 0.19 +++ P78311 381 481 AB000277 3007 3289 22.7 3.6 ++- P78311 719 740 AB000516 820 883 26.2 0.32 +++ P78311 708 742 AB002110 2065 2164 24.3 1.2 ++- P78311 449 499 AB002110 430 568 24.3 1.2 ++- P78311 369 433 AB000220 30 222 23.1 2.7 ++- P78311 1061 1098 AB000462 402 513 22.7 3.6 +++ P78311 1126 1141 AB000462 5723 5768 21.9 6.1 +++ P78311 1047 1084 AB000462 511 622 21.6 8 +++ P78311 471 493 AB000468 1716 1782 22.7 3.6 +++ P78311 368 411 AB001466 170 272 21.9 6.1 +++ P78311 392 447 AB001466 120 285 21.9 6.1 +++ P78311 1117 1132 AB001466 1835 1880 21.6 8 +++ P78312 0 1265 AB000460 351 4146 2054 0 +++ P78312 0 1265 AB000459 351 4023 1954 0 +++ P78312 0 789 AB000461 351 2718 1364 0 +++ P78312 801 1265 AB000461 2707 3976 554 0 +++ P78312 146 808 AB001563 708 2694 1130 0 +++ P78312 1171 1207 AB000509 2792 2900 43.5 2e-06 +++ P78312 1182 1207 AB000509 2960 3035 21.9 6.3 +++ P78312 1171 1206 AB000462 3770 3875 40 2e-05 ++- P78312 1061 1098 AB000462 402 513 22.7 3.7 +++ P78312 1126 1141 AB000462 5723 5768 21.9 6.3 +++ P78312 1047 1084 AB000462 511 622 21.6 8.3 +++ P78312 699 737 AB000277 263 374 26.9 0.2 +++ P78312 381 481 AB000277 3007 3289 22.7 3.7 ++- P78312 719 740 AB000516 820 883 26.2 0.33 +++ P78312 708 742 AB002110 2065 2164 24.3 1.3 ++- P78312 449 499 AB002110 430 568 24.3 1.3 ++- P78312 369 433 AB000220 30 222 23.1 2.8 +++ P78312 471 493 AB000468 1716 1782 22.7 3.7 +++ P78312 368 411 AB001466 170 272 21.9 6.3 +++ P78312 392 447 AB001466 120 285 21.9 6.3 +++ P78312 1117 1132 AB001466 1835 1880 21.6 8.3 +++ P78313 0 792 AB000461 351 2727 1375 0 +++ P78313 0 789 AB000460 351 2718 1364 0 +++ P78313 0 789 AB000459 351 2718 1364 0 +++ P78313 146 789 AB001563 708 2637 1075 0 +++ P78313 699 737 AB000277 263 374 26.9 0.12 +++ P78313 381 481 AB000277 3007 3289 22.7 2.3 +++ P78313 721 753 AB000277 3037 3133 20.8 8.6 ++- P78313 719 740 AB000516 820 883 26.2 0.2 +++ P78313 708 742 AB002110 2065 2164 24.3 0.78 ++- P78313 449 499 AB002110 430 568 24.3 0.78 ++- P78313 444 468 AB002110 507 573 21.2 6.6 ++- P78313 369 433 AB000220 30 222 23.1 1.7 +++ P78313 471 493 AB000468 1716 1782 22.7 2.3 ++- P78313 564 579 AB000468 1772 1817 20.8 8.6 +++ P78313 368 411 AB001466 170 272 21.9 3.9 +++ P78313 392 447 AB001466 120 285 21.9 3.9 +++ P78313 723 735 AB000462 195 231 20.8 8.6 +++ P78314 0 561 AB000462 261 1944 964 0 ++- P78314 249 294 AB000462 592 736 27.3 0.063 ++- P78314 292 313 AB000462 310 373 21.2 4.5 ++- P78314 257 298 AB000462 5514 5637 21.2 4.5 ++- P78314 358 418 AB000459 2986 3154 29.3 0.017 ++- P78314 358 418 AB000460 2986 3154 29.3 0.017 ++- P78314 358 418 AB000461 2939 3107 29.3 0.017 ++- P78314 268 313 AB002283 415 541 24.6 0.41 ++- P78314 294 314 AB002283 239 302 23.5 0.91 +++ P78314 265 314 AB001466 612 756 24.3 0.53 +++ P78314 262 295 AB001466 2244 2343 23.9 0.7 +++ P78314 367 405 AB001466 290 401 23.9 0.7 +++ P78314 248 313 AB001466 1421 1652 23.1 1.2 +++ P78314 378 418 AB000277 2906 3026 23.5 0.91 +++ P78314 370 428 AB000277 3011 3188 22.3 2 ++- P78314 257 269 AB000277 557 593 20.8 5.9 +++ P78314 494 516 AB000220 3899 3965 21.9 2.6 +++ P78314 376 412 AB000516 2820 2928 21.6 3.5 +++ P78314 474 485 AB000509 32 65 20.8 5.9 +++ P78314 387 418 AB000468 1559 1652 20.4 7.7 +++ P78317 0 190 AB000468 297 867 333 1e-94 +++ P78317 151 176 AB000509 225 297 31.2 0.001 +++ P78317 109 134 AB000516 2768 2843 22.3 0.56 +++ P78317 151 170 AB000449 503 560 21.2 1.3 ++- P78317 116 133 AB000277 737 785 19.6 3.6 ++- P78317 143 164 AB001466 1955 2018 18.9 6.2 +++ O00463 0 557 AB000509 54 1725 1153 0 +++ O00463 57 81 AB000468 750 825 31.2 0.004 ++- O00463 279 307 AB000468 2318 2402 22.3 2 ++- O00463 60 73 AB000468 1777 1816 20 10 ++- O00463 306 338 AB000115 1415 1511 22.7 1.5 ++- O00463 210 229 AB001106 206 263 20.4 7.6 +++ O43279 25 1087 AB000516 228 3414 1919 0 ++- O43279 757 784 AB000516 2461 2536 24.3 1.1 +++ O43279 867 971 AB001466 1385 1652 25 0.64 +++ O43279 941 960 AB001466 818 875 21.9 5.4 +++ O43279 933 971 AB000462 3070 3187 24.3 1.1 ++- O43279 950 966 AB000462 4076 4124 21.9 5.4 ++- O43279 800 829 AB000462 1941 2028 21.2 9.2 +++ O43279 917 944 AB002283 390 477 23.5 1.9 +++ O43279 594 612 AB000220 1582 1636 21.9 5.4 ++- O43279 914 954 AB000277 2744 2864 21.6 7 +++ O15100 0 134 AB000897 0 402 266 8e-75 +++ O15100 76 115 AB000468 2567 2684 19.6 2.3 ++- O15100 57 73 AB000449 1330 1378 19.6 2.3 +++ O15100 96 124 AB000462 1029 1113 18.1 6.6 ++- O15100 46 53 AB000462 3343 3364 17.7 8.6 +++ P17774 0 141 AB001106 100 523 286 8e-81 +++ P17774 78 111 AB000277 2063 2153 21.6 0.64 +++ P17774 22 64 AB000114 1192 1318 19.2 3.2 +++ P17774 71 96 AB000462 4004 4076 18.5 5.4 +++ P17774 92 103 AB002283 165 198 18.1 7.1 +++ O43281 0 561 AB001466 608 2291 850 0 +++ O43281 161 180 AB001466 2402 2459 22.7 1.6 ++- O43281 393 475 AB000462 1752 1998 26.2 0.14 ++- O43281 157 182 AB000462 4088 4211 23.1 1.2 +++ O43281 409 424 AB000459 3702 3747 21.6 3.5 ++- O43281 157 214 AB000459 3019 3196 21.6 3.5 +++ O43281 405 421 AB000459 3547 3595 20.8 5.9 +++ O43281 409 424 AB000461 3655 3700 21.6 3.5 ++- O43281 157 214 AB000461 2972 3149 21.6 3.5 +++ O43281 405 421 AB000461 3500 3548 20.8 5.9 +++ O43281 409 424 AB000460 3702 3747 21.6 3.5 ++- O43281 157 214 AB000460 3019 3196 21.6 3.5 +++ O43281 405 421 AB000460 3547 3595 20.8 5.9 +++ O43281 393 418 AB000516 2583 2658 20.4 7.7 +++ Q9UEG8 0 662 AB001563 708 2694 1130 0 +++ Q9UEG8 0 662 AB000460 789 2775 1130 0 +++ Q9UEG8 0 662 AB000459 789 2775 1130 0 +++ Q9UEG8 0 643 AB000461 789 2718 1075 0 +++ Q9UEG8 553 591 AB000277 263 374 26.9 0.099 +++ Q9UEG8 235 335 AB000277 3007 3289 22.7 1.9 +++ Q9UEG8 222 379 AB000277 2942 3341 22.7 1.9 +++ Q9UEG8 575 607 AB000277 3037 3133 20.8 7.1 ++- Q9UEG8 573 594 AB000516 820 883 26.2 0.17 +++ Q9UEG8 562 596 AB002110 2065 2164 24.3 0.64 ++- Q9UEG8 303 353 AB002110 430 568 24.3 0.64 ++- Q9UEG8 298 322 AB002110 507 573 21.2 5.4 ++- Q9UEG8 223 287 AB000220 30 222 23.1 1.4 +++ Q9UEG8 325 347 AB000468 1716 1782 22.7 1.9 ++- Q9UEG8 418 433 AB000468 1772 1817 20.8 7.1 +++ Q9UEG8 222 265 AB001466 170 272 21.9 3.2 +++ Q9UEG8 246 301 AB001466 120 285 21.9 3.2 +++ Q9UEG8 577 589 AB000462 195 231 20.8 7.1 +++ Q96Q97 0 208 AB002110 96 720 361 1e-103 +++ Q96Q97 167 203 AB000509 482 593 24.6 0.13 +++ Q96Q97 55 74 AB000460 4386 4443 21.2 1.4 ++- Q96Q97 44 74 AB000460 4398 4488 21.2 1.4 +++ Q96Q97 189 201 AB000460 4419 4455 18.9 7 +++ Q96Q97 55 74 AB000461 4216 4273 21.2 1.4 ++- Q96Q97 44 74 AB000461 4228 4318 21.2 1.4 +++ Q96Q97 189 201 AB000461 4249 4285 18.9 7 +++ Q96Q97 55 74 AB000459 4263 4320 21.2 1.4 ++- Q96Q97 44 74 AB000459 4275 4365 21.2 1.4 +++ Q96Q97 189 201 AB000459 4296 4332 18.9 7 +++ Q96Q97 48 85 AB001466 1425 1569 20.4 2.4 +++ Q96Q97 119 131 AB001466 914 950 20 3.2 ++- Q96Q97 3 9 AB001466 2202 2220 18.5 9.2 +++ Q96Q97 48 73 AB000277 3046 3112 20 3.2 +++ Q96Q97 189 201 AB000277 1884 1920 19.2 5.4 ++- Q96Q97 48 66 AB000462 3348 3402 20 3.2 +++ O60235 0 418 AB002134 61 1315 807 0 ++- O60235 351 400 AB000462 2220 2355 27.7 0.035 ++- O60235 176 205 AB000462 635 722 20.4 5.6 ++- O60235 286 379 AB000277 110 422 20.4 5.6 +++ Q9UIM1 0 139 AB002283 37 454 275 2e-77 ++- Q9UIM1 81 113 AB000277 3239 3335 21.6 0.62 +++ Q9UIM1 119 129 AB000277 2545 2575 17.7 9