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Alex for a bug: query_length doesn't get propogated.

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1 parent dcd448e commit 30fd71d85a0cf7cc54bd4a94e815bd97b822cb11 @jhannah committed Sep 15, 2011
Showing with 175 additions and 0 deletions.
  1. +156 −0 alex_s/data.blasttable
  2. +19 −0 alex_s/run.pl
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@@ -0,0 +1,156 @@
+s1-fg3-contig01519 gi|158286696|ref|XP_001688116.1| 49.23 520 259 11 166 1710 78 567 3e-87 327
+s1-fg3-contig01519 gi|157124763|ref|XP_001660512.1| 38.68 318 186 5 160 1086 61 373 5e-45 186
+s1-fg3-contig01519 gi|194753900|ref|XP_001959243.1| 34.45 299 186 6 181 1047 126 412 9e-25 119
+s1-fg3-contig01519 gi|195584501|ref|XP_002082043.1| 31.82 264 169 5 181 939 8 257 2e-22 111
+s1-fg3-contig01519 gi|195487568|ref|XP_002091963.1| 29.89 261 175 3 181 939 132 380 2e-22 111
+s1-fg3-contig01519 gi|195379951|ref|XP_002048734.1| 30.57 265 180 3 181 963 126 364 2e-22 111
+s1-fg3-contig01519 gi|195335507|ref|XP_002034405.1| 31.82 264 169 5 181 939 126 375 2e-22 111
+s1-fg3-contig01519 gi|20130109|ref|NP_611304.1| 31.30 262 171 4 181 939 126 375 3e-22 110
+s1-fg3-contig01519 gi|195155264|ref|XP_002018525.1| 28.47 274 182 4 181 960 117 371 2e-21 108
+s1-fg3-contig01519 gi|198459168|ref|XP_001361290.2| 28.47 274 182 4 181 960 117 371 2e-21 108
+s1-fg1-contig14757 gi|118785010|ref|XP_314250.3| 98.42 190 3 0 29 598 211 400 2e-164 362
+s1-fg1-contig14757 gi|118785010|ref|XP_314250.3| 99.12 113 1 0 603 941 402 514 2e-164 243
+s1-fg1-contig14757 gi|157103343|ref|XP_001647937.1| 93.72 191 12 0 29 601 211 401 3e-159 352
+s1-fg1-contig14757 gi|157103343|ref|XP_001647937.1| 93.86 114 7 0 600 941 401 514 3e-159 236
+s1-fg1-contig14757 gi|157103341|ref|XP_001647936.1| 92.67 191 14 0 29 601 209 399 2e-155 350
+s1-fg1-contig14757 gi|157103341|ref|XP_001647936.1| 89.47 114 12 0 600 941 399 512 2e-155 226
+s1-fg1-contig14757 gi|157103339|ref|XP_001647935.1| 91.10 191 17 0 29 601 210 400 1e-153 346
+s1-fg1-contig14757 gi|157103339|ref|XP_001647935.1| 89.47 114 12 0 600 941 400 513 1e-153 224
+s1-fg1-contig14757 gi|170050102|ref|XP_001859363.1| 90.58 191 18 0 29 601 210 400 2e-152 341
+s1-fg1-contig14757 gi|170050102|ref|XP_001859363.1| 90.35 114 11 0 600 941 400 513 2e-152 225
+s1-fg1-contig14757 gi|91086561|ref|XP_975997.1| 86.91 191 25 0 29 601 214 404 1e-140 323
+s1-fg1-contig14757 gi|91086561|ref|XP_975997.1| 80.70 114 22 0 600 941 404 517 1e-140 203
+s1-fg1-contig14757 gi|195124411|ref|XP_002006686.1| 84.90 192 29 0 26 601 214 405 7e-138 318
+s1-fg1-contig14757 gi|195124411|ref|XP_002006686.1| 79.82 114 23 1 600 941 405 517 7e-138 199
+s1-fg1-contig14757 gi|156541477|ref|XP_001600227.1| 81.77 192 33 1 26 595 290 481 8e-137 307
+s1-fg1-contig14757 gi|156541477|ref|XP_001600227.1| 78.81 118 25 1 588 941 479 595 8e-137 206
+s1-fg1-contig14757 gi|195381207|ref|XP_002049346.1| 84.38 192 30 0 26 601 214 405 8e-137 316
+s1-fg1-contig14757 gi|195381207|ref|XP_002049346.1| 79.82 114 23 1 600 941 405 517 8e-137 198
+s1-fg1-contig14757 gi|195442053|ref|XP_002068775.1| 83.85 192 31 0 26 601 214 405 7e-136 314
+s1-fg1-contig14757 gi|195442053|ref|XP_002068775.1| 78.07 114 25 1 600 941 405 517 7e-136 196
+s1-fg1-contig40146 gi|57954643|ref|XP_559962.1| 74.52 259 64 4 587 1357 1 257 2e-89 334
+s1-fg1-contig40146 gi|170043709|ref|XP_001849518.1| 37.17 113 63 2 611 925 7 119 3e-15 87.8
+s1-fg1-contig40146 gi|157119971|ref|XP_001653467.1| 50.72 69 34 0 611 817 19 87 3e-15 87.8
+s1-fg1-contig40146 gi|170056669|ref|XP_001864134.1| 47.89 71 37 0 614 826 10 80 1e-14 86.3
+s1-fg1-contig40146 gi|170044205|ref|XP_001849746.1| 47.83 69 36 0 611 817 20 88 4e-14 84.3
+s1-fg1-contig40146 gi|170059790|ref|XP_001865515.1| 39.29 112 68 2 605 940 4 103 1e-13 82.8
+s1-fg1-contig40146 gi|157124004|ref|XP_001654015.1| 46.48 71 38 0 614 826 10 80 1e-13 82.4
+s1-fg1-contig40146 gi|157137616|ref|XP_001664032.1| 46.48 71 38 0 614 826 10 80 1e-13 82.4
+s1-fg1-contig40146 gi|157119248|ref|XP_001653321.1| 46.25 80 43 1 587 826 1 77 2e-13 81.6
+s1-fg1-contig40146 gi|157130755|ref|XP_001661996.1| 34.78 115 69 2 611 937 9 123 2e-13 81.6
+s1-fg1-contig44761 gi|118778366|ref|XP_001237111.1| 68.10 116 36 1 2 346 122 237 2e-36 154
+s1-fg1-contig44761 gi|118778364|ref|XP_001237110.1| 69.44 108 33 0 23 346 124 231 1e-35 152
+s1-fg1-contig44761 gi|170050364|ref|XP_001861037.1| 41.38 87 50 1 68 325 126 212 2e-11 71.6
+s1-fg1-contig44761 gi|170047470|ref|XP_001851243.1| 42.31 78 44 1 95 325 1 78 1e-08 62.8
+s1-fg1-contig44761 gi|194860811|ref|XP_001969658.1| 35.23 88 57 0 83 346 98 185 2e-07 58.5
+s1-fg1-contig44761 gi|24584056|ref|NP_609624.1| 33.33 99 66 0 50 346 85 183 7e-07 56.6
+s1-fg1-contig44761 gi|198472984|ref|XP_001356132.2| 35.80 81 52 0 83 325 109 189 1e-06 56.2
+s1-fg1-contig44761 gi|195578906|ref|XP_002079304.1| 34.09 88 58 0 83 346 96 183 1e-06 56.2
+s1-fg1-contig44761 gi|195351229|ref|XP_002042138.1| 34.09 88 58 0 83 346 96 183 1e-06 56.2
+s1-fg1-contig44761 gi|195161882|ref|XP_002021787.1| 35.80 81 52 0 83 325 111 191 1e-06 56.2
+s1-fg1-contig47370 gi|5804808|emb|CAB53561.1| 40.48 84 50 1 1995 1744 189 270 2e-06 51.2
+s1-fg1-contig47370 gi|5804808|emb|CAB53561.1| 44.44 18 10 0 1690 1637 294 311 2e-06 23.9
+s1-fg1-contig47370 gi|103015|pir||B34751 34.09 132 81 3 1995 1618 567 695 1e-05 55.8
+s1-fg1-contig47370 gi|432431|gb|AAA53489.1| 29.73 111 72 2 1995 1681 638 746 4e-05 44.7
+s1-fg1-contig47370 gi|432431|gb|AAA53489.1| 55.56 18 8 0 1690 1637 743 760 4e-05 25.8
+s1-fg1-contig47370 gi|66863196|emb|CAI96735.1| 36.84 95 54 2 1971 1705 31 123 6e-05 53.9
+s1-fg1-contig47370 gi|66863194|emb|CAI96734.1| 35.79 95 55 2 1971 1705 31 123 9e-05 53.1
+s1-fg1-contig47370 gi|115752598|ref|XP_001182458.1| 34.18 79 52 1 1980 1744 469 545 1e-04 42.4
+s1-fg1-contig47370 gi|115752598|ref|XP_001182458.1| 34.62 26 17 0 1714 1637 561 586 1e-04 26.2
+s1-fg1-contig47370 gi|70907198|gb|AAZ15240.1| 43.75 64 36 0 1597 1406 674 737 3e-04 51.6
+s1-fg1-contig47370 gi|115894610|ref|XP_001180935.1| 34.25 73 48 2 1974 1756 697 767 6e-04 40.4
+s1-fg1-contig47370 gi|115894610|ref|XP_001180935.1| 55.56 18 8 0 1690 1637 795 812 6e-04 25.8
+s1-fg1-contig47371 gi|198477685|ref|XP_002136492.1| 45.45 44 24 0 724 593 262 305 1e-09 43.9
+s1-fg1-contig47371 gi|198477685|ref|XP_002136492.1| 23.28 116 89 2 585 238 308 413 1e-09 42.0
+s1-fg1-contig47371 gi|198459068|ref|XP_002136119.1| 23.28 116 89 2 585 238 308 413 3e-09 43.5
+s1-fg1-contig47371 gi|198459068|ref|XP_002136119.1| 45.00 40 22 0 724 605 262 301 3e-09 40.8
+s1-fg1-contig47371 gi|38347729|dbj|BAD01589.1| 23.91 92 70 1 585 310 288 375 7e-07 39.7
+s1-fg1-contig47371 gi|38347729|dbj|BAD01589.1| 38.64 44 27 0 724 593 242 285 7e-07 36.6
+s1-fg1-contig47371 gi|38347730|dbj|BAD01590.1| 23.91 92 70 1 585 310 288 375 7e-07 39.7
+s1-fg1-contig47371 gi|38347730|dbj|BAD01590.1| 38.64 44 27 0 724 593 242 285 7e-07 36.6
+s1-fg1-contig47371 gi|2055314|dbj|BAA57030.1| 23.91 92 70 1 585 310 374 461 7e-07 39.7
+s1-fg1-contig47371 gi|2055314|dbj|BAA57030.1| 38.64 44 27 0 724 593 328 371 7e-07 36.6
+s1-fg1-contig47371 gi|170058566|ref|XP_001864976.1| 26.40 125 92 2 585 211 436 550 9e-07 45.1
+s1-fg1-contig47371 gi|170058566|ref|XP_001864976.1| 34.09 44 29 0 724 593 390 433 9e-07 30.8
+s1-fg1-contig47371 gi|170031931|ref|XP_001843837.1| 26.40 125 92 2 585 211 436 550 9e-07 45.1
+s1-fg1-contig47371 gi|170031931|ref|XP_001843837.1| 34.09 44 29 0 724 593 390 433 9e-07 30.8
+s1-fg1-contig47371 gi|170034649|ref|XP_001845186.1| 26.72 116 85 2 585 238 436 541 1e-06 44.7
+s1-fg1-contig47371 gi|170034649|ref|XP_001845186.1| 34.09 44 29 0 724 593 390 433 1e-06 30.8
+s1-fg1-contig47371 gi|195421638|ref|XP_002060880.1| 40.91 44 26 0 724 593 105 148 4e-06 43.9
+s1-fg1-contig47371 gi|195421638|ref|XP_002060880.1| 23.40 94 70 3 585 310 151 237 4e-06 30.0
+s1-fg1-contig47371 gi|195457394|ref|XP_002075550.1| 34.09 44 29 0 724 593 175 218 2e-05 37.7
+s1-fg1-contig47371 gi|195457394|ref|XP_002075550.1| 23.91 92 70 2 585 310 221 307 2e-05 33.5
+s1-fg1-contig65215 gi|118785010|ref|XP_314250.3| 52.35 149 58 4 3 410 513 649 2e-30 136
+s1-fg1-contig65215 gi|157103343|ref|XP_001647937.1| 46.76 139 71 2 3 410 513 649 6e-25 118
+s1-fg1-contig65215 gi|157103341|ref|XP_001647936.1| 46.76 139 71 2 3 410 511 647 8e-24 114
+s1-fg1-contig65215 gi|170050108|ref|XP_001859378.1| 45.14 144 71 4 3 410 513 647 5e-23 111
+s1-fg1-contig65215 gi|170050104|ref|XP_001859368.1| 46.81 141 70 2 3 410 511 647 5e-23 111
+s1-fg1-contig65215 gi|157103339|ref|XP_001647935.1| 41.61 149 74 4 3 410 512 648 8e-21 104
+s1-fg1-contig65215 gi|170050102|ref|XP_001859363.1| 40.94 149 75 4 3 410 512 648 2e-20 102
+s1-fg1-contig65215 gi|194754603|ref|XP_001959584.1| 63.08 65 24 0 53 247 528 592 3e-18 95.9
+s1-fg1-contig65215 gi|194754603|ref|XP_001959584.1| 30.20 149 91 5 3 410 516 647 2e-10 70.1
+s1-fg1-contig65215 gi|195335623|ref|XP_002034463.1| 63.08 65 24 0 53 247 528 592 7e-18 94.7
+s1-fg1-contig65215 gi|195335623|ref|XP_002034463.1| 34.03 144 87 6 3 410 516 647 3e-11 72.8
+s1-fg1-contig65215 gi|219416526|ref|XP_002206070.1| 67.80 59 19 0 71 247 510 568 1e-17 93.6
+s1-fg1-contig65215 gi|219416526|ref|XP_002206070.1| 31.54 149 89 5 3 410 490 623 9e-12 74.3
+s1-fg1-contig72430 gi|158296356|ref|XP_001231056.2| 90.48 84 8 0 1205 954 3 86 1e-36 159
+s1-fg1-contig72430 gi|170029587|ref|XP_001842673.1| 50.68 148 72 2 1193 753 109 246 3e-27 127
+s1-fg1-contig72430 gi|157104293|ref|XP_001648340.1| 44.20 181 87 4 1325 825 52 205 8e-27 126
+s1-fg1-contig72430 gi|17384023|emb|CAD11912.1| 50.00 130 65 2 1190 801 137 247 8e-22 109
+s1-fg1-contig72430 gi|119370784|sp|Q1KKX7.1|HXB3A_FUGRU 60.23 88 32 1 1262 1008 186 273 2e-21 108
+s1-fg1-contig72430 gi|158702228|gb|ABW77445.1| 35.62 233 145 7 1208 525 132 348 3e-21 107
+s1-fg1-contig72430 gi|195947350|ref|NP_001124326.1| 35.62 233 145 7 1208 525 132 348 3e-21 107
+s1-fg1-contig72430 gi|220898204|gb|ACL81458.1| 46.77 124 64 3 1319 954 127 235 4e-21 107
+s1-fg1-contig72430 gi|217035822|gb|ACJ74380.1| 60.22 93 37 2 1295 1017 102 192 4e-21 107
+s1-fg1-contig72430 gi|219485588|ref|XP_002239814.1| 56.57 99 43 2 1313 1017 194 289 4e-21 107
+s1-fg1-contig86439 gi|7159363|gb|AAF36974.2|AF230521_1 56.76 185 79 4 1541 990 1 181 6e-41 172
+s1-fg1-contig86439 gi|170029595|ref|XP_001842677.1| 72.50 80 22 1 1550 1311 297 374 3e-24 117
+s1-fg1-contig86439 gi|195152063|ref|XP_002016958.1| 58.82 102 40 2 1556 1257 282 381 6e-23 113
+s1-fg1-contig86439 gi|27374286|gb|AAO01040.1| 58.82 102 40 2 1556 1257 278 378 8e-23 112
+s1-fg1-contig86439 gi|15450325|gb|AAK96032.1| 63.53 85 31 0 1565 1311 170 254 1e-22 112
+s1-fg1-contig86439 gi|2708301|gb|AAB92411.1| 70.89 79 23 0 1526 1290 40 118 1e-22 112
+s1-fg1-contig86439 gi|86515424|ref|NP_001034539.1| 63.53 85 31 0 1565 1311 170 254 1e-22 112
+s1-fg1-contig86439 gi|541626|gb|AAC46491.1| 63.53 85 31 0 1565 1311 170 254 1e-22 112
+s1-fg1-contig86439 gi|213515508|ref|NP_001133039.1| 72.60 73 20 0 1523 1305 127 199 1e-22 112
+s1-fg1-contig86439 gi|164430223|gb|ABY55439.1| 57.89 95 38 1 1526 1248 257 351 3e-22 110
+s1-fg5-contig108581 gi|158290640|ref|XP_563445.3| 81.89 127 22 2 760 383 693 814 5e-72 185
+s1-fg5-contig108581 gi|158290640|ref|XP_563445.3| 83.05 59 10 0 369 193 820 878 5e-72 112
+s1-fg5-contig108581 gi|157119618|ref|XP_001659452.1| 59.32 118 48 3 736 383 708 809 1e-49 113
+s1-fg5-contig108581 gi|157119618|ref|XP_001659452.1| 72.06 68 19 0 369 166 815 882 1e-49 109
+s1-fg5-contig108581 gi|170033102|ref|XP_001844418.1| 72.13 61 17 0 565 383 849 909 3e-45 105
+s1-fg5-contig108581 gi|170033102|ref|XP_001844418.1| 80.00 55 11 0 369 205 915 969 3e-45 103
+s1-fg5-contig108581 gi|110761880|ref|XP_001121767.1| 54.32 81 37 0 616 374 722 802 1e-41 98.6
+s1-fg5-contig108581 gi|110761880|ref|XP_001121767.1| 72.73 55 15 0 369 205 805 859 1e-41 97.8
+s1-fg5-contig108581 gi|156541423|ref|XP_001602590.1| 74.55 55 14 0 369 205 952 1006 1e-40 99.4
+s1-fg5-contig108581 gi|156541423|ref|XP_001602590.1| 70.37 54 16 0 535 374 896 949 1e-40 93.2
+s1-fg5-contig108581 gi|189237979|ref|XP_001812268.1| 82.22 45 8 0 345 211 737 781 2e-38 93.2
+s1-fg5-contig108581 gi|189237979|ref|XP_001812268.1| 63.16 57 21 0 544 374 670 726 2e-38 92.0
+s1-fg5-contig108581 gi|212513350|gb|EEB15941.1| 70.37 54 16 0 369 208 950 1003 1e-34 92.8
+s1-fg5-contig108581 gi|212513350|gb|EEB15941.1| 48.53 68 35 0 592 389 875 942 1e-34 79.7
+s1-fg5-contig108581 gi|195401859|ref|XP_002059528.1| 34.01 147 76 4 763 386 1322 1463 9e-30 86.3
+s1-fg5-contig108581 gi|195401859|ref|XP_002059528.1| 48.00 75 38 2 345 124 1479 1545 9e-30 70.1
+s1-fg5-contig108581 gi|195045297|ref|XP_001991948.1| 38.28 128 70 3 742 386 1458 1574 3e-29 85.5
+s1-fg5-contig108581 gi|195045297|ref|XP_001991948.1| 46.67 75 39 2 345 124 1590 1656 3e-29 68.9
+s1-fg5-contig108581 gi|195129946|ref|XP_002009415.1| 35.16 128 74 2 742 386 1337 1462 1e-27 80.5
+s1-fg5-contig108581 gi|195129946|ref|XP_002009415.1| 55.56 54 23 1 345 187 1478 1531 1e-27 68.6
+s1-fg1-contig130549 gi|158300317|ref|XP_001689242.1| 46.48 71 24 2 784 614 60 130 5e-04 50.8
+s1-fg4-contig131511 gi|118792950|ref|XP_320599.3| 84.87 304 41 2 1 897 138 440 7e-143 511
+s1-fg4-contig131511 gi|46948842|gb|AAT07320.1| 95.09 285 9 1 58 897 3 287 2e-140 504
+s1-fg4-contig131511 gi|170069518|ref|XP_001869253.1| 62.05 303 110 5 4 897 140 427 7e-101 372
+s1-fg4-contig131511 gi|170069516|ref|XP_001869252.1| 61.72 303 111 5 4 897 140 427 2e-100 371
+s1-fg4-contig131511 gi|157137998|ref|XP_001664112.1| 58.88 304 120 5 1 897 141 430 4e-94 350
+s1-fg4-contig131511 gi|157120906|ref|XP_001659788.1| 46.05 304 159 7 1 897 137 414 4e-68 263
+s1-fg4-contig131511 gi|195028314|ref|XP_001987021.1| 42.07 309 169 10 1 897 152 439 3e-61 240
+s1-fg4-contig131511 gi|198456050|ref|XP_001360218.2| 39.47 304 179 7 1 897 177 458 5e-60 236
+s1-fg4-contig131511 gi|195431563|ref|XP_002063806.1| 39.41 307 178 8 1 897 172 456 1e-59 235
+s1-fg4-contig131511 gi|194885679|ref|XP_001976476.1| 39.80 304 178 7 1 897 172 454 1e-59 235
+s1-fg1-contig152121 gi|118778366|ref|XP_001237111.1| 72.48 109 30 0 1491 1817 130 238 2e-28 131
+s1-fg1-contig152121 gi|118778364|ref|XP_001237110.1| 70.64 109 32 0 1491 1817 124 232 1e-27 129
+s1-fg1-contig152121 gi|170050364|ref|XP_001861037.1| 44.83 87 47 1 1536 1793 126 212 2e-06 58.9
+s1-fg1-contig152121 gi|194860811|ref|XP_001969658.1| 35.87 92 59 0 1551 1826 98 189 2e-05 55.1
+s1-fg1-contig152121 gi|198472984|ref|XP_001356132.2| 35.80 81 52 0 1551 1793 109 189 9e-05 53.1
+s1-fg1-contig152121 gi|195161882|ref|XP_002021787.1| 35.80 81 52 0 1551 1793 111 191 9e-05 53.1
+s1-fg1-contig152121 gi|195351229|ref|XP_002042138.1| 34.78 92 60 0 1551 1826 96 187 1e-04 52.8
+s1-fg1-contig152121 gi|24584056|ref|NP_609624.1| 34.78 92 60 0 1551 1826 96 187 1e-04 52.8
+s1-fg1-contig152121 gi|195472544|ref|XP_002088560.1| 33.70 92 61 0 1551 1826 96 187 3e-04 51.6
+s1-fg1-contig152121 gi|195578906|ref|XP_002079304.1| 35.23 88 57 0 1551 1814 96 183 3e-04 51.2
View
@@ -0,0 +1,19 @@
+#!/usr/bin/perl
+
+use strict;
+use warnings;
+
+use Bio::SearchIO;
+
+my ($blast_file) = shift @ARGV;
+
+my $search_io = Bio::SearchIO->new(-file => $blast_file,
+ -format => 'blasttable') or die "Blast file parsing failed.";
+
+while (my $result = $search_io->next_result) {
+ print $result->query_length, "\n";
+}
+
+
+
+

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