/usr/share/perl5/Bio/SearchIO/blast.pm is in libbio-perl-perl 1.6.924-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 | #
# BioPerl module for Bio::SearchIO::blast
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
# 20030409 - sac
# PSI-BLAST full parsing support. Rollout of new
# model which will remove Steve's old psiblast driver
# 20030424 - jason
# Megablast parsing fix as reported by Neil Saunders
# 20030427 - jason
# Support bl2seq parsing
# 20031124 - jason
# Parse more blast statistics, lambda, entropy, etc
# from WU-BLAST in frame-specific manner
# 20060216 - cjf - fixed blast parsing for BLAST v2.2.13 output
# 20071104 - dmessina - added support for WUBLAST -echofilter
# 20071121 - cjf - fixed several bugs (bugs 2391, 2399, 2409)
=head1 NAME
Bio::SearchIO::blast - Event generator for event based parsing of
blast reports
=head1 SYNOPSIS
# Do not use this object directly - it is used as part of the
# Bio::SearchIO system.
use Bio::SearchIO;
my $searchio = Bio::SearchIO->new(-format => 'blast',
-file => 't/data/ecolitst.bls');
while( my $result = $searchio->next_result ) {
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
# ...
}
}
}
=head1 DESCRIPTION
This object encapsulated the necessary methods for generating events
suitable for building Bio::Search objects from a BLAST report file.
Read the L<Bio::SearchIO> for more information about how to use this.
This driver can parse:
=over 4
=item *
NCBI produced plain text BLAST reports from blastall, this also
includes PSIBLAST, PSITBLASTN, RPSBLAST, and bl2seq reports. NCBI XML
BLAST output is parsed with the blastxml SearchIO driver
=item *
WU-BLAST all reports
=item *
Jim Kent's BLAST-like output from his programs (BLASTZ, BLAT)
=item *
BLAST-like output from Paracel BTK output
=back
=head2 bl2seq parsing
Since I cannot differentiate between BLASTX and TBLASTN since bl2seq
doesn't report the algorithm used - I assume it is BLASTX by default -
you can supply the program type with -report_type in the SearchIO
constructor i.e.
my $parser = Bio::SearchIO->new(-format => 'blast',
-file => 'bl2seq.tblastn.report',
-report_type => 'tblastn');
This only really affects where the frame and strand information are
put - they will always be on the $hsp-E<gt>query instead of on the
$hsp-E<gt>hit part of the feature pair for blastx and tblastn bl2seq
produced reports. Hope that's clear...
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Jason Stajich
Email Jason Stajich jason-at-bioperl.org
=head1 CONTRIBUTORS
Steve Chervitz sac-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...'
package Bio::SearchIO::blast;
use Bio::SearchIO::IteratedSearchResultEventBuilder;
use strict;
use vars qw(%MAPPING %MODEMAP
$DEFAULT_BLAST_WRITER_CLASS
$MAX_HSP_OVERLAP
$DEFAULT_SIGNIF
$DEFAULT_SCORE
$DEFAULTREPORTTYPE
);
use base qw(Bio::SearchIO);
use Data::Dumper;
BEGIN {
# mapping of NCBI Blast terms to Bioperl hash keys
%MODEMAP = (
'BlastOutput' => 'result',
'Iteration' => 'iteration',
'Hit' => 'hit',
'Hsp' => 'hsp'
);
# This should really be done more intelligently, like with
# XSLT
%MAPPING = (
'Hsp_bit-score' => 'HSP-bits',
'Hsp_score' => 'HSP-score',
'Hsp_evalue' => 'HSP-evalue',
'Hsp_n', => 'HSP-n',
'Hsp_pvalue' => 'HSP-pvalue',
'Hsp_query-from' => 'HSP-query_start',
'Hsp_query-to' => 'HSP-query_end',
'Hsp_hit-from' => 'HSP-hit_start',
'Hsp_hit-to' => 'HSP-hit_end',
'Hsp_positive' => 'HSP-conserved',
'Hsp_identity' => 'HSP-identical',
'Hsp_gaps' => 'HSP-hsp_gaps',
'Hsp_hitgaps' => 'HSP-hit_gaps',
'Hsp_querygaps' => 'HSP-query_gaps',
'Hsp_qseq' => 'HSP-query_seq',
'Hsp_hseq' => 'HSP-hit_seq',
'Hsp_midline' => 'HSP-homology_seq',
'Hsp_align-len' => 'HSP-hsp_length',
'Hsp_query-frame' => 'HSP-query_frame',
'Hsp_hit-frame' => 'HSP-hit_frame',
'Hsp_links' => 'HSP-links',
'Hsp_group' => 'HSP-hsp_group',
'Hsp_features' => 'HSP-hit_features',
'Hit_id' => 'HIT-name',
'Hit_len' => 'HIT-length',
'Hit_accession' => 'HIT-accession',
'Hit_def' => 'HIT-description',
'Hit_signif' => 'HIT-significance',
# For NCBI blast, the description line contains bits.
# For WU-blast, the description line contains score.
'Hit_score' => 'HIT-score',
'Hit_bits' => 'HIT-bits',
'Iteration_iter-num' => 'ITERATION-number',
'Iteration_converged' => 'ITERATION-converged',
'BlastOutput_program' => 'RESULT-algorithm_name',
'BlastOutput_version' => 'RESULT-algorithm_version',
'BlastOutput_algorithm-reference' => 'RESULT-algorithm_reference',
'BlastOutput_rid' => 'RESULT-rid',
'BlastOutput_query-def' => 'RESULT-query_name',
'BlastOutput_query-len' => 'RESULT-query_length',
'BlastOutput_query-acc' => 'RESULT-query_accession',
'BlastOutput_query-gi' => 'RESULT-query_gi',
'BlastOutput_querydesc' => 'RESULT-query_description',
'BlastOutput_db' => 'RESULT-database_name',
'BlastOutput_db-len' => 'RESULT-database_entries',
'BlastOutput_db-let' => 'RESULT-database_letters',
'BlastOutput_inclusion-threshold' => 'RESULT-inclusion_threshold',
'Parameters_matrix' => { 'RESULT-parameters' => 'matrix' },
'Parameters_expect' => { 'RESULT-parameters' => 'expect' },
'Parameters_include' => { 'RESULT-parameters' => 'include' },
'Parameters_sc-match' => { 'RESULT-parameters' => 'match' },
'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch' },
'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen' },
'Parameters_gap-extend' => { 'RESULT-parameters' => 'gapext' },
'Parameters_filter' => { 'RESULT-parameters' => 'filter' },
'Parameters_allowgaps' => { 'RESULT-parameters' => 'allowgaps' },
'Parameters_full_dbpath' => { 'RESULT-parameters' => 'full_dbpath' },
'Statistics_db-len' => { 'RESULT-statistics' => 'dbentries' },
'Statistics_db-let' => { 'RESULT-statistics' => 'dbletters' },
'Statistics_hsp-len' =>
{ 'RESULT-statistics' => 'effective_hsplength' },
'Statistics_query-len' => { 'RESULT-statistics' => 'querylength' },
'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace' },
'Statistics_eff-spaceused' =>
{ 'RESULT-statistics' => 'effectivespaceused' },
'Statistics_eff-dblen' =>
{ 'RESULT-statistics' => 'effectivedblength' },
'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' },
'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' },
'Statistics_entropy' => { 'RESULT-statistics' => 'entropy' },
'Statistics_gapped_kappa' => { 'RESULT-statistics' => 'kappa_gapped' },
'Statistics_gapped_lambda' =>
{ 'RESULT-statistics' => 'lambda_gapped' },
'Statistics_gapped_entropy' =>
{ 'RESULT-statistics' => 'entropy_gapped' },
'Statistics_framewindow' =>
{ 'RESULT-statistics' => 'frameshiftwindow' },
'Statistics_decay' => { 'RESULT-statistics' => 'decayconst' },
'Statistics_hit_to_db' => { 'RESULT-statistics' => 'Hits_to_DB' },
'Statistics_num_suc_extensions' =>
{ 'RESULT-statistics' => 'num_successful_extensions' },
'Statistics_length_adjustment' => { 'RESULT-statistics' => 'length_adjustment' },
'Statistics_number_of_hsps_better_than_expect_value_cutoff_without_gapping' =>
{ 'RESULT-statistics' => 'number_of_hsps_better_than_expect_value_cutoff_without_gapping' },
'Statistics_number_of_hsps_gapped' => { 'RESULT-statistics' => 'number_of_hsps_gapped' },
'Statistics_number_of_hsps_successfully_gapped' => { 'RESULT-statistics' => 'number_of_hsps_successfully_gapped' },
# WU-BLAST stats
'Statistics_DFA_states' => { 'RESULT-statistics' => 'num_dfa_states' },
'Statistics_DFA_size' => { 'RESULT-statistics' => 'dfa_size' },
'Statistics_noprocessors' =>
{ 'RESULT-statistics' => 'no_of_processors' },
'Statistics_neighbortime' =>
{ 'RESULT-statistics' => 'neighborhood_generate_time' },
'Statistics_starttime' => { 'RESULT-statistics' => 'start_time' },
'Statistics_endtime' => { 'RESULT-statistics' => 'end_time' },
);
# add WU-BLAST Frame-Based Statistics
for my $frame ( 0 .. 3 ) {
for my $strand ( '+', '-' ) {
for my $ind (
qw(length efflength E S W T X X_gapped E2
E2_gapped S2)
)
{
$MAPPING{"Statistics_frame$strand$frame\_$ind"} =
{ 'RESULT-statistics' => "Frame$strand$frame\_$ind" };
}
for my $val (qw(lambda kappa entropy )) {
for my $type (qw(used computed gapped)) {
my $key = "Statistics_frame$strand$frame\_$val\_$type";
my $val =
{ 'RESULT-statistics' =>
"Frame$strand$frame\_$val\_$type" };
$MAPPING{$key} = $val;
}
}
}
}
# add Statistics
for my $stats (
qw(T A X1 X2 X3 S1 S2 X1_bits X2_bits X3_bits
S1_bits S2_bits num_extensions
num_successful_extensions
seqs_better_than_cutoff
posted_date
search_cputime total_cputime
search_actualtime total_actualtime
no_of_processors ctxfactor)
)
{
my $key = "Statistics_$stats";
my $val = { 'RESULT-statistics' => $stats };
$MAPPING{$key} = $val;
}
# add WU-BLAST Parameters
for my $param (
qw(span span1 span2 links warnings notes hspsepsmax
hspsepqmax topcomboN topcomboE postsw cpus wordmask
filter sort_by_pvalue sort_by_count sort_by_highscore
sort_by_totalscore sort_by_subjectlength noseqs gi qtype
qres V B Z Y M N)
)
{
my $key = "Parameters_$param";
my $val = { 'RESULT-parameters' => $param };
$MAPPING{$key} = $val;
}
$DEFAULT_BLAST_WRITER_CLASS = 'Bio::SearchIO::Writer::HitTableWriter';
$MAX_HSP_OVERLAP = 2; # Used when tiling multiple HSPs.
$DEFAULTREPORTTYPE = 'BLASTP'; # for bl2seq
}
=head2 new
Title : new
Usage : my $obj = Bio::SearchIO::blast->new(%args);
Function: Builds a new Bio::SearchIO::blast object
Returns : Bio::SearchIO::blast
Args : Key-value pairs:
-fh/-file => filehandle/filename to BLAST file
-format => 'blast'
-report_type => 'blastx', 'tblastn', etc -- only for bl2seq
reports when you want to distinguish between
tblastn and blastx reports (this only controls
where the frame information is put - on the query
or subject object.
-inclusion_threshold => e-value threshold for inclusion in the
PSI-BLAST score matrix model (blastpgp)
-signif => float or scientific notation number to be used
as a P- or Expect value cutoff
-score => integer or scientific notation number to be used
as a blast score value cutoff
-bits => integer or scientific notation number to be used
as a bit score value cutoff
-hit_filter => reference to a function to be used for
filtering hits based on arbitrary criteria.
All hits of each BLAST report must satisfy
this criteria to be retained.
If a hit fails this test, it is ignored.
This function should take a
Bio::Search::Hit::BlastHit.pm object as its first
argument and return true
if the hit should be retained.
Sample filter function:
-hit_filter => sub { $hit = shift;
$hit->gaps == 0; },
(Note: -filt_func is synonymous with -hit_filter)
-overlap => integer. The amount of overlap to permit between
adjacent HSPs when tiling HSPs. A reasonable value is 2.
Default = $Bio::SearchIO::blast::MAX_HSP_OVERLAP.
The following criteria are not yet supported:
(these are probably best applied within this module rather than in the
event handler since they would permit the parser to take some shortcuts.)
-check_all_hits => boolean. Check all hits for significance against
significance criteria. Default = false.
If false, stops processing hits after the first
non-significant hit or the first hit that fails
the hit_filter call. This speeds parsing,
taking advantage of the fact that the hits
are processed in the order they appear in the report.
-min_query_len => integer to be used as a minimum for query sequence length.
Reports with query sequences below this length will
not be processed. Default = no minimum length.
-best => boolean. Only process the best hit of each report;
default = false.
=cut
sub _initialize {
my ( $self, @args ) = @_;
$self->SUPER::_initialize(@args);
# Blast reports require a specialized version of the SREB due to the
# possibility of iterations (PSI-BLAST). Forwarding all arguments to it. An
# issue here is that we want to set new default object factories if none are
# supplied.
my $handler = Bio::SearchIO::IteratedSearchResultEventBuilder->new(@args);
$self->attach_EventHandler($handler);
# 2006-04-26 move this to the attach_handler function in this module so we
# can really reset the handler
# Optimization: caching
# the EventHandler since it is used a lot during the parse.
# $self->{'_handler_cache'} = $handler;
my ($rpttype ) = $self->_rearrange(
[
qw(
REPORT_TYPE)
],
@args
);
defined $rpttype && ( $self->{'_reporttype'} = $rpttype );
}
sub attach_EventHandler {
my ($self,$handler) = @_;
$self->SUPER::attach_EventHandler($handler);
# Optimization: caching the EventHandler since it is used a lot
# during the parse.
$self->{'_handler_cache'} = $handler;
return;
}
=head2 next_result
Title : next_result
Usage : my $hit = $searchio->next_result;
Function: Returns the next Result from a search
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub next_result {
my ($self) = @_;
my $v = $self->verbose;
my $data = '';
my $flavor = '';
$self->{'_seentop'} = 0; # start next report at top
my ( $reporttype, $seenquery, $reportline, $reportversion );
my ( $seeniteration, $found_again );
my $incl_threshold = $self->inclusion_threshold;
my $bl2seq_fix;
$self->start_document(); # let the fun begin...
my (@hit_signifs);
my $gapped_stats = 0; # for switching between gapped/ungapped
# lambda, K, H
local $_ = "\n"; #consistency
PARSER:
while ( defined( $_ = $self->_readline ) ) {
next if (/^\s+$/); # skip empty lines
next if (/CPU time:/);
next if (/^>\s*$/);
next if (/[*]+\s+No hits found\s+[*]+/);
if (
/^((?:\S+?)?BLAST[NPX]?)\s+(.+)$/i # NCBI BLAST, PSIBLAST
# RPSBLAST, MEGABLAST
|| /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i #Paracel BTK
)
{
($reporttype, $reportversion) = ($1, $2);
# need to keep track of whether this is WU-BLAST
if ($reportversion && $reportversion =~ m{WashU$}) {
$self->{'_wublast'}++;
}
$self->debug("blast.pm: Start of new report: $reporttype, $reportversion\n");
if ( $self->{'_seentop'} ) {
# This handles multi-result input streams
$self->_pushback($_);
last PARSER;
}
$self->_start_blastoutput;
if ($reporttype =~ /RPS-BLAST/) {
$reporttype .= '(BLASTP)'; # default RPS-BLAST type
}
$reportline = $_; # to fix the fact that RPS-BLAST output is wrong
$self->element(
{
'Name' => 'BlastOutput_program',
'Data' => $reporttype
}
);
$self->element(
{
'Name' => 'BlastOutput_version',
'Data' => $reportversion
}
);
$self->element(
{
'Name' => 'BlastOutput_inclusion-threshold',
'Data' => $incl_threshold
}
);
}
# parse the BLAST algorithm reference
elsif(/^Reference:\s+(.*)$/) {
# want to preserve newlines for the BLAST algorithm reference
my $algorithm_reference = "$1\n";
$_ = $self->_readline;
# while the current line, does not match an empty line, a RID:, a
# Database:, or a query definition line (Query=) we are still
# looking at the algorithm_reference, append it to what we parsed so
# far
while($_ !~ /^$/ && $_ !~ /^RID:/ && $_ !~ /^Database:/ && $_ !~ /^Query=/) {
$algorithm_reference .= "$_";
$_ = $self->_readline;
}
# if we exited the while loop, we saw an empty line, a RID:, or a
# Database:, so push it back
$self->_pushback($_);
$self->element(
{
'Name' => 'BlastOutput_algorithm-reference',
'Data' => $algorithm_reference
}
);
}
# parse BLAST RID (Request ID)
elsif(/^RID:\s+(.*)$/) {
my $rid = $1;
$self->element(
{
'Name' => 'BlastOutput_rid',
'Data' => $rid
}
);
}
# added Windows workaround for bug 1985
elsif (/^(Searching|Results from round)/) {
next unless $1 =~ /Results from round/;
$self->debug("blast.pm: Possible psi blast iterations found...\n");
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->in_element('hit')
&& $self->end_element( { 'Name' => 'Hit' } );
if ( defined $seeniteration ) {
$self->within_element('iteration')
&& $self->end_element( { 'Name' => 'Iteration' } );
$self->start_element( { 'Name' => 'Iteration' } );
}
else {
$self->start_element( { 'Name' => 'Iteration' } );
}
$seeniteration = 1;
}
elsif (/^Query=\s*(.*)$/) {
my $q = $1;
$self->debug("blast.pm: Query= found...$_\n");
my $size = 0;
if ( defined $seenquery ) {
$self->_pushback($_);
$self->_pushback($reportline) if $reportline;
last PARSER;
}
if ( !defined $reporttype ) {
$self->_start_blastoutput;
if ( defined $seeniteration ) {
$self->in_element('iteration')
&& $self->end_element( { 'Name' => 'Iteration' } );
$self->start_element( { 'Name' => 'Iteration' } );
}
else {
$self->start_element( { 'Name' => 'Iteration' } );
}
$seeniteration = 1;
}
$seenquery = $q;
$_ = $self->_readline;
while ( defined($_) ) {
if (/^Database:/) {
$self->_pushback($_);
last;
}
# below line fixes length issue with BLAST v2.2.13; still works
# with BLAST v2.2.12
if ( /\((\-?[\d,]+)\s+letters.*\)/ || /^Length=(\-?[\d,]+)/ ) {
$size = $1;
$size =~ s/,//g;
last;
}
else {
# bug 2391
$q .= ($q =~ /\w$/ && $_ =~ /^\w/) ? " $_" : $_;
$q =~ s/\s+/ /g; # this catches the newline as well
$q =~ s/^ | $//g;
}
$_ = $self->_readline;
}
chomp($q);
my ( $nm, $desc ) = split( /\s+/, $q, 2 );
$self->element(
{
'Name' => 'BlastOutput_query-def',
'Data' => $nm
}
) if $nm;
$self->element(
{
'Name' => 'BlastOutput_query-len',
'Data' => $size
}
);
defined $desc && $desc =~ s/\s+$//;
$self->element(
{
'Name' => 'BlastOutput_querydesc',
'Data' => $desc
}
);
my ( $gi, $acc, $version ) = $self->_get_seq_identifiers($nm);
$version = defined($version) && length($version) ? ".$version" : "";
$self->element(
{
'Name' => 'BlastOutput_query-acc',
'Data' => "$acc$version"
}
) if $acc;
# these elements are dropped with some multiquery reports; add
# back here
$self->element(
{
'Name' => 'BlastOutput_db-len',
'Data' => $self->{'_blsdb_length'}
}
) if $self->{'_blsdb_length'};
$self->element(
{
'Name' => 'BlastOutput_db-let',
'Data' => $self->{'_blsdb_letters'}
}
) if $self->{'_blsdb_letters'};
$self->element(
{
'Name' => 'BlastOutput_db',
'Data' => $self->{'_blsdb'}
}
) if $self->{'_blsdb_letters'};
}
# added check for WU-BLAST -echofilter option (bug 2388)
elsif (/^>Unfiltered[+-]1$/) {
# skip all of the lines of unfiltered sequence
while($_ !~ /^Database:/) {
$self->debug("Bypassing features line: $_");
$_ = $self->_readline;
}
$self->_pushback($_);
}
elsif (/Sequences producing significant alignments:/) {
$self->debug("blast.pm: Processing NCBI-BLAST descriptions\n");
$flavor = 'ncbi';
# PSI-BLAST parsing needs to be fixed to specifically look
# for old vs new per iteration, as sorting based on duplication
# leads to bugs, see bug 1986
# The next line is not necessarily whitespace in psiblast reports.
# Also note that we must look for the end of this section by testing
# for a line with a leading >. Blank lines occur with this section
# for psiblast.
if ( !$self->in_element('iteration') ) {
$self->start_element( { 'Name' => 'Iteration' } );
}
# changed 8/28/2008 to exit hit table if blank line is found after an
# appropriate line
my $h_regex;
my $seen_block;
DESCLINE:
while ( defined( my $descline = $self->_readline() ) ) {
if ($descline =~ m{^\s*$}) {
last DESCLINE if $seen_block;
next DESCLINE;
}
# any text match is part of block...
$seen_block++;
# GCG multiline oddness...
if ($descline =~ /^(\S+)\s+Begin:\s\d+\s+End:\s+\d+/xms) {
my ($id, $nextline) = ($1, $self->_readline);
$nextline =~ s{^!}{};
$descline = "$id $nextline";
}
# NCBI style hit table (no N)
if ($descline =~ /(?<!cor) # negative lookahead
(\d*\.?(?:[\+\-eE]+)?\d+) # number (float or scientific notation)
\s+ # space
(\d*\.?(?:[\+\-eE]+)?\d+) # number (float or scientific notation)
\s*$/xms) {
my ( $score, $evalue ) = ($1, $2);
# Some data clean-up so e-value will appear numeric to perl
$evalue =~ s/^e/1e/i;
# This to handle no-HSP case
my @line = split ' ',$descline;
# we want to throw away the score, evalue
pop @line, pop @line;
# and N if it is present (of course they are not
# really in that order, but it doesn't matter
if ($3) { pop @line }
# add the last 2 entries s.t. we can reconstruct
# a minimal Hit object at the end of the day
push @hit_signifs, [ $evalue, $score, shift @line, join( ' ', @line ) ];
} elsif ($descline =~ /^CONVERGED/i) {
$self->element(
{
'Name' => 'Iteration_converged',
'Data' => 1
}
);
} else {
$self->_pushback($descline); # Catch leading > (end of section)
last DESCLINE;
}
}
}
elsif (/Sequences producing High-scoring Segment Pairs:/) {
# This block is for WU-BLAST, so we don't have to check for psi-blast stuff
# skip the next line
$self->debug("blast.pm: Processing WU-BLAST descriptions\n");
$_ = $self->_readline();
$flavor = 'wu';
if ( !$self->in_element('iteration') ) {
$self->start_element( { 'Name' => 'Iteration' } );
}
while ( defined( $_ = $self->_readline() )
&& !/^\s+$/ )
{
my @line = split;
pop @line; # throw away first number which is for 'N'col
# add the last 2 entries to array s.t. we can reconstruct
# a minimal Hit object at the end of the day
push @hit_signifs,
[ pop @line, pop @line, shift @line, join( ' ', @line ) ];
}
}
elsif (/^Database:\s*(.+?)\s*$/) {
$self->debug("blast.pm: Database: $1\n");
my $db = $1;
while ( defined( $_ = $self->_readline ) ) {
if (
/^\s+(\-?[\d\,]+|\S+)\s+sequences\;
\s+(\-?[\d,]+|\S+)\s+ # Deal with NCBI 2.2.8 OSX problems
total\s+letters/ox
)
{
my ( $s, $l ) = ( $1, $2 );
$s =~ s/,//g;
$l =~ s/,//g;
$self->element(
{
'Name' => 'BlastOutput_db-len',
'Data' => $s
}
);
$self->element(
{
'Name' => 'BlastOutput_db-let',
'Data' => $l
}
);
# cache for next round in cases with multiple queries
$self->{'_blsdb'} = $db;
$self->{'_blsdb_length'} = $s;
$self->{'_blsdb_letters'} = $l;
last;
}
else {
chomp;
$db .= $_;
}
}
$self->element(
{
'Name' => 'BlastOutput_db',
'Data' => $db
}
);
}
# move inside of a hit
elsif (/^(?:Subject=|>)\s*(\S+)\s*(.*)?/) {
chomp;
$self->debug("blast.pm: Hit: $1\n");
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->in_element('hit')
&& $self->end_element( { 'Name' => 'Hit' } );
# special case when bl2seq reports don't have a leading
# Query=
if ( !$self->within_element('result') ) {
$self->_start_blastoutput;
$self->start_element( { 'Name' => 'Iteration' } );
}
elsif ( !$self->within_element('iteration') ) {
$self->start_element( { 'Name' => 'Iteration' } );
}
$self->start_element( { 'Name' => 'Hit' } );
my $id = $1;
my $restofline = $2;
$self->debug("Starting a hit: $1 $2\n");
$self->element(
{
'Name' => 'Hit_id',
'Data' => $id
}
);
my ($gi, $acc, $version ) = $self->_get_seq_identifiers($id);
$self->element(
{
'Name' => 'Hit_accession',
'Data' => $acc
}
);
# add hit significance (from the hit table)
# this is where Bug 1986 went awry
# Changed for Bug2409; hit->significance and hit->score/bits derived
# from HSPs, not hit table unless necessary
HITTABLE:
while (my $v = shift @hit_signifs) {
my $tableid = $v->[2];
if ($tableid !~ m{\Q$id\E}) {
$self->debug("Hit table ID $tableid doesn't match current hit id $id, checking next hit table entry...\n");
next HITTABLE;
} else {
last HITTABLE;
}
}
while ( defined( $_ = $self->_readline() ) ) {
next if (/^\s+$/);
chomp;
if (/Length\s*=\s*([\d,]+)/) {
my $l = $1;
$l =~ s/\,//g;
$self->element(
{
'Name' => 'Hit_len',
'Data' => $l
}
);
last;
}
else {
if ($restofline !~ /\s$/) { # bug #3235
s/^\s(?!\s)/\x01/; #new line to concatenate desc lines with <soh>
}
$restofline .= ($restofline =~ /\w$/ && $_ =~ /^\w/) ? " $_" : $_;
$restofline =~ s/\s+/ /g; # this catches the newline as well
$restofline =~ s/^ | $//g;
}
}
$restofline =~ s/\s+/ /g;
$self->element(
{
'Name' => 'Hit_def',
'Data' => $restofline
}
);
}
elsif (/\s+(Plus|Minus) Strand HSPs:/i) {
next;
}
elsif (
( $self->in_element('hit') || $self->in_element('hsp') )
&& # paracel genewise BTK
m/Score\s*=\s*(\S+)\s*bits\s* # Bit score
(?:\((\d+)\))?, # Raw score
\s+Log\-Length\sScore\s*=\s*(\d+) # Log-Length score
/ox
)
{
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->start_element( { 'Name' => 'Hsp' } );
$self->debug( "Got paracel genewise HSP score=$1\n");
# Some data clean-up so e-value will appear numeric to perl
my ( $bits, $score, $evalue ) = ( $1, $2, $3 );
$evalue =~ s/^e/1e/i;
$self->element(
{
'Name' => 'Hsp_score',
'Data' => $score
}
);
$self->element(
{
'Name' => 'Hsp_bit-score',
'Data' => $bits
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => $evalue
}
);
}
elsif (
( $self->in_element('hit') || $self->in_element('hsp') )
&& # paracel hframe BTK
m/Score\s*=\s*([^,\s]+), # Raw score
\s*Expect\s*=\s*([^,\s]+), # E-value
\s*P(?:\(\S+\))?\s*=\s*([^,\s]+) # P-value
/ox
)
{
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->start_element( { 'Name' => 'Hsp' } );
$self->debug( "Got paracel hframe HSP score=$1\n");
# Some data clean-up so e-value will appear numeric to perl
my ( $score, $evalue, $pvalue ) = ( $1, $2, $3 );
$evalue = "1$evalue" if $evalue =~ /^e/;
$pvalue = "1$pvalue" if $pvalue =~ /^e/;
$self->element(
{
'Name' => 'Hsp_score',
'Data' => $score
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => $evalue
}
);
$self->element(
{
'Name' => 'Hsp_pvalue',
'Data' => $pvalue
}
);
}
elsif (
( $self->in_element('hit') || $self->in_element('hsp') )
&& # wublast
m/Score\s*=\s*(\S+)\s* # Bit score
\(([\d\.]+)\s*bits\), # Raw score
\s*Expect\s*=\s*([^,\s]+), # E-value
\s*(?:Sum)?\s* # SUM
P(?:\(\d+\))?\s*=\s*([^,\s]+) # P-value
(?:\s*,\s+Group\s*\=\s*(\d+))? # HSP Group
/ox
)
{ # wu-blast HSP parse
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->start_element( { 'Name' => 'Hsp' } );
# Some data clean-up so e-value will appear numeric to perl
my ( $score, $bits, $evalue, $pvalue, $group ) =
( $1, $2, $3, $4, $5 );
$evalue =~ s/^e/1e/i;
$pvalue =~ s/^e/1e/i;
$self->element(
{
'Name' => 'Hsp_score',
'Data' => $score
}
);
$self->element(
{
'Name' => 'Hsp_bit-score',
'Data' => $bits
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => $evalue
}
);
$self->element(
{
'Name' => 'Hsp_pvalue',
'Data' => $pvalue
}
);
if ( defined $group ) {
$self->element(
{
'Name' => 'Hsp_group',
'Data' => $group
}
);
}
}
elsif (
( $self->in_element('hit') || $self->in_element('hsp') )
&& # ncbi blast, works with 2.2.17
m/^\sFeatures\s\w+\sthis\spart/xmso
# If the line begins with "Features in/flanking this part of subject sequence:"
)
{
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
my $featline;
$_ = $self->_readline;
while($_ !~ /^\s*$/) {
chomp;
$featline .= $_;
$_ = $self->_readline;
}
$self->_pushback($_);
$featline =~ s{(?:^\s+|\s+^)}{}g;
$featline =~ s{\n}{;}g;
$self->start_element( { 'Name' => 'Hsp' } );
$self->element(
{
'Name' => 'Hsp_features',
'Data' => $featline
}
);
$self->{'_seen_hsp_features'} = 1;
}
elsif (
( $self->in_element('hit') || $self->in_element('hsp') )
&& # ncbi blast, works with 2.2.17
m/Score\s*=\s*(\S+)\s*bits\s* # Bit score
(?:\((\d+)\))?, # Missing for BLAT pseudo-BLAST fmt
\s*Expect(?:\((\d+\+?)\))?\s*=\s*([^,\s]+) # E-value
/ox
)
{ # parse NCBI blast HSP
if( !$self->{'_seen_hsp_features'} ) {
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->start_element( { 'Name' => 'Hsp' } );
}
# Some data clean-up so e-value will appear numeric to perl
my ( $bits, $score, $n, $evalue ) = ( $1, $2, $3, $4 );
$evalue =~ s/^e/1e/i;
$self->element(
{
'Name' => 'Hsp_score',
'Data' => $score
}
);
$self->element(
{
'Name' => 'Hsp_bit-score',
'Data' => $bits
}
);
$self->element(
{
'Name' => 'Hsp_evalue',
'Data' => $evalue
}
);
$self->element(
{
'Name' => 'Hsp_n',
'Data' => $n
}
) if defined $n;
$score = '' unless defined $score; # deal with BLAT which
# has no score only bits
$self->debug("Got NCBI HSP score=$score, evalue $evalue\n");
}
elsif (
$self->in_element('hsp')
&& m/Identities\s*=\s*(\d+)\s*\/\s*(\d+)\s*[\d\%\(\)]+\s*
(?:,\s*Positives\s*=\s*(\d+)\/(\d+)\s*[\d\%\(\)]+\s*)? # pos only valid for Protein alignments
(?:\,\s*Gaps\s*=\s*(\d+)\/(\d+))? # Gaps
/oxi
)
{
$self->element(
{
'Name' => 'Hsp_identity',
'Data' => $1
}
);
$self->element(
{
'Name' => 'Hsp_align-len',
'Data' => $2
}
);
if ( defined $3 ) {
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => $3
}
);
}
else {
$self->element(
{
'Name' => 'Hsp_positive',
'Data' => $1
}
);
}
if ( defined $6 ) {
$self->element(
{
'Name' => 'Hsp_gaps',
'Data' => $5
}
);
}
$self->{'_Query'} = { 'begin' => 0, 'end' => 0 };
$self->{'_Sbjct'} = { 'begin' => 0, 'end' => 0 };
if (/(Frame\s*=\s*.+)$/) {
# handle wu-blast Frame listing on same line
$self->_pushback($1);
}
}
elsif ( $self->in_element('hsp')
&& /Strand\s*=\s*(Plus|Minus)\s*\/\s*(Plus|Minus)/i )
{
# consume this event ( we infer strand from start/end)
if (!defined($reporttype)) {
$self->{'_reporttype'} = $reporttype = 'BLASTN';
$bl2seq_fix = 1; # special case to resubmit the algorithm
# reporttype
}
next;
}
elsif ( $self->in_element('hsp')
&& /Links\s*=\s*(\S+)/ox )
{
$self->element(
{
'Name' => 'Hsp_links',
'Data' => $1
}
);
}
elsif ( $self->in_element('hsp')
&& /Frame\s*=\s*([\+\-][1-3])\s*(\/\s*([\+\-][1-3]))?/ )
{
my $frame1 = $1 || 0;
my $frame2 = $2 || 0;
# this is for bl2seq only
if ( not defined $reporttype ) {
$bl2seq_fix = 1;
if ( $frame1 && $frame2 ) {
$reporttype = 'TBLASTX'
}
else {
# We can distinguish between BLASTX and TBLASTN from the report
# (and assign $frame1 properly) by using the start/end from query.
# If the report is BLASTX, the coordinates distance from query
# will be 3 times the length of the alignment shown (coordinates in nt,
# alignment in aa); if not then subject is the nucleotide sequence (TBLASTN).
# Will have to fast-forward to query alignment line and then go back.
my $fh = $self->_fh;
my $file_pos = tell $fh;
my $a_position = '';
my $ali_length = '';
my $b_position = '';
while (my $line = <$fh>) {
if ($line =~ m/^(?:Query|Sbjct):?\s+(\-?\d+)?\s*(\S+)\s+(\-?\d+)?/) {
$a_position = $1;
my $alignment = $2;
$b_position = $3;
use Bio::LocatableSeq;
my $gap_symbols = $Bio::LocatableSeq::GAP_SYMBOLS;
$alignment =~ s/[$gap_symbols]//g;
$ali_length = length($alignment);
last;
}
}
my $coord_length = ($a_position < $b_position) ? ($b_position - $a_position + 1)
: ($a_position - $b_position + 1);
($coord_length == ($ali_length * 3)) ? ($reporttype = 'BLASTX') : ($reporttype = 'TBLASTN');
# Rewind filehandle to its original position to continue parsing
seek $fh, $file_pos, 0;
}
$self->{'_reporttype'} = $reporttype;
}
my ( $queryframe, $hitframe );
if ( $reporttype eq 'TBLASTX' ) {
( $queryframe, $hitframe ) = ( $frame1, $frame2 );
$hitframe =~ s/\/\s*//g;
}
elsif ( $reporttype eq 'TBLASTN' || $reporttype eq 'PSITBLASTN') {
( $hitframe, $queryframe ) = ( $frame1, 0 );
}
elsif ( $reporttype eq 'BLASTX' || $reporttype eq 'RPS-BLAST(BLASTP)') {
( $queryframe, $hitframe ) = ( $frame1, 0 );
# though NCBI doesn't report it, this is a special BLASTX-like
# RPS-BLAST; should be handled differently
if ($reporttype eq 'RPS-BLAST(BLASTP)') {
$self->element(
{
'Name' => 'BlastOutput_program',
'Data' => 'RPS-BLAST(BLASTX)'
}
);
}
}
$self->element(
{
'Name' => 'Hsp_query-frame',
'Data' => $queryframe
}
);
$self->element(
{
'Name' => 'Hsp_hit-frame',
'Data' => $hitframe
}
);
}
elsif (/^Parameters:/
|| /^\s+Database:\s+?/
|| /^\s+Subset/
|| /^\s*Lambda/
|| /^\s*Histogram/
|| ( $self->in_element('hsp') && /WARNING|NOTE/ ) )
{
# Note: Lambda check was necessary to parse
# t/data/ecoli_domains.rpsblast AND to parse bl2seq
$self->debug("blast.pm: found parameters section \n");
$self->in_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->in_element('hit')
&& $self->end_element( { 'Name' => 'Hit' } );
# This is for the case when we specify -b 0 (or B=0 for WU-BLAST)
# and still want to construct minimal Hit objects
$self->_cleanup_hits(\@hit_signifs) if scalar(@hit_signifs);
$self->within_element('iteration')
&& $self->end_element( { 'Name' => 'Iteration' } );
next if /^\s+Subset/;
my $blast = (/^(\s+Database\:)|(\s*Lambda)/) ? 'ncbi' : 'wublast';
if (/^\s*Histogram/) {
$blast = 'btk';
}
my $last = '';
# default is that gaps are allowed
$self->element(
{
'Name' => 'Parameters_allowgaps',
'Data' => 'yes'
}
);
while ( defined( $_ = $self->_readline ) ) {
# If Lambda/Kappa/Entropy numbers appear first at this point,
# pushback and add the header line to process it correctly
if (/^\s+[\d+\.]+\s+[\d+\.]+\s+[\d+\.]/ and $last eq '') {
$self->_pushback($_);
$self->_pushback("Lambda K H\n");
next;
}
elsif (
/^((?:\S+)?BLAST[NPX]?)\s+(.+)$/i # NCBI BLAST, PSIBLAST
# RPSBLAST, MEGABLAST
|| /^(P?GENEWISE|HFRAME|SWN|TSWN)\s+(.+)/i #Paracel BTK
)
{
$self->_pushback($_);
# let's handle this in the loop
last;
}
elsif (/^Query=/) {
$self->_pushback($_);
$self->_pushback($reportline) if $reportline;
last PARSER;
}
# here is where difference between wublast and ncbiblast
# is better handled by different logic
if ( /Number of Sequences:\s+([\d\,]+)/i
|| /of sequences in database:\s+(\-?[\d,]+)/i )
{
my $c = $1;
$c =~ s/\,//g;
$self->element(
{
'Name' => 'Statistics_db-len',
'Data' => $c
}
);
}
elsif (/letters in database:\s+(\-?[\d,]+)/i) {
my $s = $1;
$s =~ s/,//g;
$self->element(
{
'Name' => 'Statistics_db-let',
'Data' => $s
}
);
}
elsif ( $blast eq 'btk' ) {
next;
}
elsif ( $blast eq 'wublast' ) {
# warn($_);
if (/E=(\S+)/) {
$self->element(
{
'Name' => 'Parameters_expect',
'Data' => $1
}
);
}
elsif (/nogaps/) {
$self->element(
{
'Name' => 'Parameters_allowgaps',
'Data' => 'no'
}
);
}
elsif (/ctxfactor=(\S+)/) {
$self->element(
{
'Name' => 'Statistics_ctxfactor',
'Data' => $1
}
);
}
elsif (
/(postsw|links|span[12]?|warnings|notes|gi|noseqs|qres|qype)/
)
{
$self->element(
{
'Name' => "Parameters_$1",
'Data' => 'yes'
}
);
}
elsif (/(\S+)=(\S+)/) {
$self->element(
{
'Name' => "Parameters_$1",
'Data' => $2
}
);
}
elsif ( $last =~ /(Frame|Strand)\s+MatID\s+Matrix name/i ) {
my $firstgapinfo = 1;
my $frame = undef;
while ( defined($_) && !/^\s+$/ ) {
s/^\s+//;
s/\s+$//;
if ( $firstgapinfo
&& s/Q=(\d+),R=(\d+)\s+//x )
{
$firstgapinfo = 0;
$self->element(
{
'Name' => 'Parameters_gap-open',
'Data' => $1
}
);
$self->element(
{
'Name' => 'Parameters_gap-extend',
'Data' => $2
}
);
my @fields = split;
for my $type (
qw(lambda_gapped
kappa_gapped
entropy_gapped)
)
{
next if $type eq 'n/a';
if ( !@fields ) {
warn "fields is empty for $type\n";
next;
}
$self->element(
{
'Name' =>
"Statistics_frame$frame\_$type",
'Data' => shift @fields
}
);
}
}
else {
my ( $frameo, $matid, $matrix, @fields ) =
split;
if ( !defined $frame ) {
# keep some sort of default feature I guess
# even though this is sort of wrong
$self->element(
{
'Name' => 'Parameters_matrix',
'Data' => $matrix
}
);
$self->element(
{
'Name' => 'Statistics_lambda',
'Data' => $fields[0]
}
);
$self->element(
{
'Name' => 'Statistics_kappa',
'Data' => $fields[1]
}
);
$self->element(
{
'Name' => 'Statistics_entropy',
'Data' => $fields[2]
}
);
}
$frame = $frameo;
my $ii = 0;
for my $type (
qw(lambda_used
kappa_used
entropy_used
lambda_computed
kappa_computed
entropy_computed)
)
{
my $f = $fields[$ii];
next unless defined $f; # deal with n/a
if ( $f eq 'same' ) {
$f = $fields[ $ii - 3 ];
}
$ii++;
$self->element(
{
'Name' =>
"Statistics_frame$frame\_$type",
'Data' => $f
}
);
}
}
# get the next line
$_ = $self->_readline;
}
$last = $_;
}
elsif ( $last =~ /(Frame|Strand)\s+MatID\s+Length/i ) {
my $frame = undef;
while ( defined($_) && !/^\s+/ ) {
s/^\s+//;
s/\s+$//;
my @fields = split;
if ( @fields <= 3 ) {
for my $type (qw(X_gapped E2_gapped S2)) {
last unless @fields;
$self->element(
{
'Name' =>
"Statistics_frame$frame\_$type",
'Data' => shift @fields
}
);
}
}
else {
for my $type (
qw(length
efflength
E S W T X E2 S2)
)
{
$self->element(
{
'Name' =>
"Statistics_frame$frame\_$type",
'Data' => shift @fields
}
);
}
}
$_ = $self->_readline;
}
$last = $_;
}
elsif (/(\S+\s+\S+)\s+DFA:\s+(\S+)\s+\((.+)\)/) {
if ( $1 eq 'states in' ) {
$self->element(
{
'Name' => 'Statistics_DFA_states',
'Data' => "$2 $3"
}
);
}
elsif ( $1 eq 'size of' ) {
$self->element(
{
'Name' => 'Statistics_DFA_size',
'Data' => "$2 $3"
}
);
}
}
elsif (
m/^\s+Time to generate neighborhood:\s+
(\S+\s+\S+\s+\S+)/x
)
{
$self->element(
{
'Name' => 'Statistics_neighbortime',
'Data' => $1
}
);
}
elsif (/processors\s+used:\s+(\d+)/) {
$self->element(
{
'Name' => 'Statistics_noprocessors',
'Data' => $1
}
);
}
elsif (
m/^\s+(\S+)\s+cpu\s+time:\s+ # cputype
(\S+\s+\S+\s+\S+) # cputime
\s+Elapsed:\s+(\S+)/x
)
{
my $cputype = lc($1);
$self->element(
{
'Name' => "Statistics_$cputype\_cputime",
'Data' => $2
}
);
$self->element(
{
'Name' => "Statistics_$cputype\_actualtime",
'Data' => $3
}
);
}
elsif (/^\s+Start:/) {
my ( $junk, $start, $stime, $end, $etime ) =
split( /\s+(Start|End)\:\s+/, $_ );
chomp($stime);
$self->element(
{
'Name' => 'Statistics_starttime',
'Data' => $stime
}
);
chomp($etime);
$self->element(
{
'Name' => 'Statistics_endtime',
'Data' => $etime
}
);
}
elsif (/^\s+Database:\s+(.+)$/) {
$self->element(
{
'Name' => 'Parameters_full_dbpath',
'Data' => $1
}
);
}
elsif (/^\s+Posted:\s+(.+)/) {
my $d = $1;
chomp($d);
$self->element(
{
'Name' => 'Statistics_posted_date',
'Data' => $d
}
);
}
}
elsif ( $blast eq 'ncbi' ) {
if (m/^Matrix:\s+(.+)\s*$/oxi) {
$self->element(
{
'Name' => 'Parameters_matrix',
'Data' => $1
}
);
}
elsif (/^Gapped/) {
$gapped_stats = 1;
}
elsif (/^Lambda/) {
$_ = $self->_readline;
s/^\s+//;
my ( $lambda, $kappa, $entropy ) = split;
if ($gapped_stats) {
$self->element(
{
'Name' => "Statistics_gapped_lambda",
'Data' => $lambda
}
);
$self->element(
{
'Name' => "Statistics_gapped_kappa",
'Data' => $kappa
}
);
$self->element(
{
'Name' => "Statistics_gapped_entropy",
'Data' => $entropy
}
);
}
else {
$self->element(
{
'Name' => "Statistics_lambda",
'Data' => $lambda
}
);
$self->element(
{
'Name' => "Statistics_kappa",
'Data' => $kappa
}
);
$self->element(
{
'Name' => "Statistics_entropy",
'Data' => $entropy
}
);
}
}
elsif (m/effective\s+search\s+space\s+used:\s+(\d+)/oxi) {
$self->element(
{
'Name' => 'Statistics_eff-spaceused',
'Data' => $1
}
);
}
elsif (m/effective\s+search\s+space:\s+(\d+)/oxi) {
$self->element(
{
'Name' => 'Statistics_eff-space',
'Data' => $1
}
);
}
elsif (
m/Gap\s+Penalties:\s+Existence:\s+(\d+)\,
\s+Extension:\s+(\d+)/ox
)
{
$self->element(
{
'Name' => 'Parameters_gap-open',
'Data' => $1
}
);
$self->element(
{
'Name' => 'Parameters_gap-extend',
'Data' => $2
}
);
}
elsif (/effective\s+HSP\s+length:\s+(\d+)/) {
$self->element(
{
'Name' => 'Statistics_hsp-len',
'Data' => $1
}
);
}
elsif (/Number\s+of\s+HSP's\s+better\s+than\s+(\S+)\s+without\s+gapping:\s+(\d+)/) {
$self->element(
{
'Name' => 'Statistics_number_of_hsps_better_than_expect_value_cutoff_without_gapping',
'Data' => $2
}
);
}
elsif (/Number\s+of\s+HSP's\s+gapped:\s+(\d+)/) {
$self->element(
{
'Name' => 'Statistics_number_of_hsps_gapped',
'Data' => $1
}
);
}
elsif (/Number\s+of\s+HSP's\s+successfully\s+gapped:\s+(\d+)/) {
$self->element(
{
'Name' => 'Statistics_number_of_hsps_successfully_gapped',
'Data' => $1
}
);
}
elsif (/Length\s+adjustment:\s+(\d+)/) {
$self->element(
{
'Name' => 'Statistics_length_adjustment',
'Data' => $1
}
);
}
elsif (/effective\s+length\s+of\s+query:\s+([\d\,]+)/i) {
my $c = $1;
$c =~ s/\,//g;
$self->element(
{
'Name' => 'Statistics_query-len',
'Data' => $c
}
);
}
elsif (/effective\s+length\s+of\s+database:\s+([\d\,]+)/i) {
my $c = $1;
$c =~ s/\,//g;
$self->element(
{
'Name' => 'Statistics_eff-dblen',
'Data' => $c
}
);
}
elsif (
/^(T|A|X1|X2|X3|S1|S2):\s+(\d+(\.\d+)?)\s+(?:\(\s*(\d+\.\d+) bits\))?/
)
{
my $v = $2;
chomp($v);
$self->element(
{
'Name' => "Statistics_$1",
'Data' => $v
}
);
if ( defined $4 ) {
$self->element(
{
'Name' => "Statistics_$1_bits",
'Data' => $4
}
);
}
}
elsif (
m/frameshift\s+window\,
\s+decay\s+const:\s+(\d+)\,\s+([\.\d]+)/x
)
{
$self->element(
{
'Name' => 'Statistics_framewindow',
'Data' => $1
}
);
$self->element(
{
'Name' => 'Statistics_decay',
'Data' => $2
}
);
}
elsif (m/^Number\s+of\s+Hits\s+to\s+DB:\s+(\S+)/ox) {
$self->element(
{
'Name' => 'Statistics_hit_to_db',
'Data' => $1
}
);
}
elsif (m/^Number\s+of\s+extensions:\s+(\S+)/ox) {
$self->element(
{
'Name' => 'Statistics_num_extensions',
'Data' => $1
}
);
}
elsif (
m/^Number\s+of\s+successful\s+extensions:\s+
(\S+)/ox
)
{
$self->element(
{
'Name' => 'Statistics_num_suc_extensions',
'Data' => $1
}
);
}
elsif (
m/^Number\s+of\s+sequences\s+better\s+than\s+
(\S+):\s+(\d+)/ox
)
{
$self->element(
{
'Name' => 'Parameters_expect',
'Data' => $1
}
);
$self->element(
{
'Name' => 'Statistics_seqs_better_than_cutoff',
'Data' => $2
}
);
}
elsif (/^\s+Posted\s+date:\s+(.+)/) {
my $d = $1;
chomp($d);
$self->element(
{
'Name' => 'Statistics_posted_date',
'Data' => $d
}
);
}
elsif ( !/^\s+$/ ) {
#$self->debug( "unmatched stat $_");
}
}
$last = $_;
}
} elsif ( $self->in_element('hsp') ) {
$self->debug("blast.pm: Processing HSP\n");
# let's read 3 lines at a time;
# bl2seq hackiness... Not sure I like
$self->{'_reporttype'} ||= $DEFAULTREPORTTYPE;
my %data = (
'Query' => '',
'Mid' => '',
'Hit' => ''
);
my $len;
for ( my $i = 0 ; defined($_) && $i < 3 ; $i++ ) {
# $self->debug("$i: $_") if $v;
if ( ( $i == 0 && /^\s+$/) ||
/^\s*(?:Lambda|Minus|Plus|Score)/i
) {
$self->_pushback($_) if defined $_;
$self->end_element( { 'Name' => 'Hsp' } );
last;
}
chomp;
if (/^((Query|Sbjct):?\s+(\-?\d+)?\s*)(\S+)\s+(\-?\d+)?/) {
my ( $full, $type, $start, $str, $end ) =
( $1, $2, $3, $4, $5 );
if ( $str eq '-' ) {
$i = 3 if $type eq 'Sbjct';
}
else {
$data{$type} = $str;
}
$len = length($full);
$self->{"\_$type"}->{'begin'} = $start
unless $self->{"_$type"}->{'begin'};
$self->{"\_$type"}->{'end'} = $end;
} elsif (/^((Query|Sbjct):?\s+(\-?0+)\s*)/) {
# Bug from NCBI's BLAST: unaligned output
$_ = $self->_readline() for 0..1;
last;
} else {
$self->throw("no data for midline $_")
unless ( defined $_ && defined $len );
$data{'Mid'} = substr( $_, $len );
}
$_ = $self->_readline();
}
$self->characters(
{
'Name' => 'Hsp_qseq',
'Data' => $data{'Query'}
}
);
$self->characters(
{
'Name' => 'Hsp_hseq',
'Data' => $data{'Sbjct'}
}
);
$self->characters(
{
'Name' => 'Hsp_midline',
'Data' => $data{'Mid'}
}
);
}
else {
#$self->debug("blast.pm: unrecognized line $_");
}
}
$self->debug("blast.pm: End of BlastOutput\n");
if ( $self->{'_seentop'} ) {
$self->within_element('hsp')
&& $self->end_element( { 'Name' => 'Hsp' } );
$self->within_element('hit')
&& $self->end_element( { 'Name' => 'Hit' } );
# cleanup extra hits
$self->_cleanup_hits(\@hit_signifs) if scalar(@hit_signifs);
$self->within_element('iteration')
&& $self->end_element( { 'Name' => 'Iteration' } );
if ($bl2seq_fix) {
$self->element(
{
'Name' => 'BlastOutput_program',
'Data' => $reporttype
}
);
}
$self->end_element( { 'Name' => 'BlastOutput' } );
}
return $self->end_document();
}
# Private method for internal use only.
sub _start_blastoutput {
my $self = shift;
$self->start_element( { 'Name' => 'BlastOutput' } );
$self->{'_seentop'} = 1;
$self->{'_result_count'}++;
$self->{'_handler_rc'} = undef;
}
=head2 _will_handle
Title : _will_handle
Usage : Private method. For internal use only.
if( $self->_will_handle($type) ) { ... }
Function: Provides an optimized way to check whether or not an element of a
given type is to be handled.
Returns : Reference to EventHandler object if the element type is to be handled.
undef if the element type is not to be handled.
Args : string containing type of element.
Optimizations:
=over 2
=item 1
Using the cached pointer to the EventHandler to minimize repeated
lookups.
=item 2
Caching the will_handle status for each type that is encountered so
that it only need be checked by calling
handler-E<gt>will_handle($type) once.
=back
This does not lead to a major savings by itself (only 5-10%). In
combination with other optimizations, or for large parse jobs, the
savings good be significant.
To test against the unoptimized version, remove the parentheses from
around the third term in the ternary " ? : " operator and add two
calls to $self-E<gt>_eventHandler().
=cut
sub _will_handle {
my ( $self, $type ) = @_;
my $handler = $self->{'_handler_cache'};
my $will_handle =
defined( $self->{'_will_handle_cache'}->{$type} )
? $self->{'_will_handle_cache'}->{$type}
: ( $self->{'_will_handle_cache'}->{$type} =
$handler->will_handle($type) );
return $will_handle ? $handler : undef;
}
=head2 start_element
Title : start_element
Usage : $eventgenerator->start_element
Function: Handles a start element event
Returns : none
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub start_element {
my ( $self, $data ) = @_;
# we currently don't care about attributes
my $nm = $data->{'Name'};
my $type = $MODEMAP{$nm};
if ($type) {
my $handler = $self->_will_handle($type);
if ($handler) {
my $func = sprintf( "start_%s", lc $type );
$self->{'_handler_rc'} = $handler->$func( $data->{'Attributes'} );
}
#else {
#$self->debug( # changed 4/29/2006 to play nice with other event handlers
# "Bio::SearchIO::InternalParserError ".
# "\nCan't handle elements of type \'$type.\'"
#);
#}
unshift @{ $self->{'_elements'} }, $type;
if ( $type eq 'result' ) {
$self->{'_values'} = {};
$self->{'_result'} = undef;
} else {
# cleanup some things
if ( defined $self->{'_values'} ) {
foreach my $k (
grep { /^\U$type\-/ }
keys %{ $self->{'_values'} }
)
{
delete $self->{'_values'}->{$k};
}
}
}
}
}
=head2 end_element
Title : end_element
Usage : $eventgenerator->end_element
Function: Handles an end element event
Returns : hashref with an element's worth of data
Args : hashref with at least 2 keys 'Data' and 'Name'
=cut
sub end_element {
my ( $self, $data ) = @_;
my $nm = $data->{'Name'};
my $type;
my $rc;
# cache these (TODO: we should probably cache all cross-report data)
if ( $nm eq 'BlastOutput_program' ) {
if ( $self->{'_last_data'} =~ /(t?blast[npx])/i ) {
$self->{'_reporttype'} = uc $1;
}
$self->{'_reporttype'} ||= $DEFAULTREPORTTYPE;
}
if ( $nm eq 'BlastOutput_version' ) {
$self->{'_reportversion'} = $self->{'_last_data'};
}
# Hsps are sort of weird, in that they end when another
# object begins so have to detect this in end_element for now
if ( $nm eq 'Hsp' ) {
foreach (qw(Hsp_qseq Hsp_midline Hsp_hseq Hsp_features)) {
$self->element(
{
'Name' => $_,
'Data' => $self->{'_last_hspdata'}->{$_}
}
) if defined $self->{'_last_hspdata'}->{$_};
}
$self->{'_last_hspdata'} = {};
$self->element(
{
'Name' => 'Hsp_query-from',
'Data' => $self->{'_Query'}->{'begin'}
}
);
$self->element(
{
'Name' => 'Hsp_query-to',
'Data' => $self->{'_Query'}->{'end'}
}
);
$self->element(
{
'Name' => 'Hsp_hit-from',
'Data' => $self->{'_Sbjct'}->{'begin'}
}
);
$self->element(
{
'Name' => 'Hsp_hit-to',
'Data' => $self->{'_Sbjct'}->{'end'}
}
);
# } elsif( $nm eq 'Iteration' ) {
# Nothing special needs to be done here.
}
if ( $type = $MODEMAP{$nm} ) {
my $handler = $self->_will_handle($type);
if ($handler) {
my $func = sprintf( "end_%s", lc $type );
$rc = $handler->$func( $self->{'_reporttype'}, $self->{'_values'} );
}
shift @{ $self->{'_elements'} };
}
elsif ( $MAPPING{$nm} ) {
if ( ref( $MAPPING{$nm} ) =~ /hash/i ) {
# this is where we shove in the data from the
# hashref info about params or statistics
my $key = ( keys %{ $MAPPING{$nm} } )[0];
$self->{'_values'}->{$key}->{ $MAPPING{$nm}->{$key} } =
$self->{'_last_data'};
}
else {
$self->{'_values'}->{ $MAPPING{$nm} } = $self->{'_last_data'};
}
}
else {
#$self->debug("blast.pm: unknown nm $nm, ignoring\n");
}
$self->{'_last_data'} = ''; # remove read data if we are at
# end of an element
$self->{'_result'} = $rc if ( defined $type && $type eq 'result' );
$self->{'_seen_hsp_features'} = 0;
return $rc;
}
=head2 element
Title : element
Usage : $eventhandler->element({'Name' => $name, 'Data' => $str});
Function: Convenience method that calls start_element, characters, end_element
Returns : none
Args : Hash ref with the keys 'Name' and 'Data'
=cut
sub element {
my ( $self, $data ) = @_;
# Note that start element isn't needed for character data
# Not too SAX-y, though
#$self->start_element($data);
$self->characters($data);
$self->end_element($data);
}
=head2 characters
Title : characters
Usage : $eventgenerator->characters($str)
Function: Send a character events
Returns : none
Args : string
=cut
sub characters {
my ( $self, $data ) = @_;
if ( $self->in_element('hsp')
&& $data->{'Name'} =~ /^Hsp\_(qseq|hseq|midline)$/ )
{
$self->{'_last_hspdata'}->{ $data->{'Name'} } .= $data->{'Data'}
if defined $data->{'Data'};
}
return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
$self->{'_last_data'} = $data->{'Data'};
}
=head2 within_element
Title : within_element
Usage : if( $eventgenerator->within_element($element) ) {}
Function: Test if we are within a particular element
This is different than 'in' because within can be tested
for a whole block.
Returns : boolean
Args : string element name
See Also: L<in_element>
=cut
sub within_element {
my ( $self, $name ) = @_;
return 0
if ( !defined $name && !defined $self->{'_elements'}
|| scalar @{ $self->{'_elements'} } == 0 );
foreach ( @{ $self->{'_elements'} } ) {
if ( $_ eq $name ) {
return 1;
}
}
return 0;
}
=head2 in_element
Title : in_element
Usage : if( $eventgenerator->in_element($element) ) {}
Function: Test if we are in a particular element
This is different than 'within_element' because within
can be tested for a whole block.
Returns : boolean
Args : string element name
See Also: L<within_element>
=cut
sub in_element {
my ( $self, $name ) = @_;
return 0 if !defined $self->{'_elements'}->[0];
return ( $self->{'_elements'}->[0] eq $name );
}
=head2 start_document
Title : start_document
Usage : $eventgenerator->start_document
Function: Handle a start document event
Returns : none
Args : none
=cut
sub start_document {
my ($self) = @_;
$self->{'_lasttype'} = '';
$self->{'_values'} = {};
$self->{'_result'} = undef;
$self->{'_elements'} = [];
}
=head2 end_document
Title : end_document
Usage : $eventgenerator->end_document
Function: Handles an end document event
Returns : Bio::Search::Result::ResultI object
Args : none
=cut
sub end_document {
my ( $self, @args ) = @_;
#$self->debug("blast.pm: end_document\n");
return $self->{'_result'};
}
sub write_result {
my ( $self, $blast, @args ) = @_;
if ( not defined( $self->writer ) ) {
$self->warn("Writer not defined. Using a $DEFAULT_BLAST_WRITER_CLASS");
$self->writer( $DEFAULT_BLAST_WRITER_CLASS->new() );
}
$self->SUPER::write_result( $blast, @args );
}
sub result_count {
my $self = shift;
return $self->{'_result_count'};
}
sub report_count { shift->result_count }
=head2 inclusion_threshold
Title : inclusion_threshold
Usage : my $incl_thresh = $isreb->inclusion_threshold;
: $isreb->inclusion_threshold(1e-5);
Function: Get/Set the e-value threshold for inclusion in the PSI-BLAST
score matrix model (blastpgp) that was used for generating the reports
being parsed.
Returns : number (real)
Default value: $Bio::SearchIO::IteratedSearchResultEventBuilder::DEFAULT_INCLUSION_THRESHOLD
Args : number (real) (e.g., 0.0001 or 1e-4 )
=cut
=head2 max_significance
Usage : $obj->max_significance();
Purpose : Set/Get the P or Expect value used as significance screening cutoff.
This is the value of the -signif parameter supplied to new().
Hits with P or E-value above this are skipped.
Returns : Scientific notation number with this format: 1.0e-05.
Argument : Scientific notation number or float (when setting)
Comments : Screening of significant hits uses the data provided on the
: description line. For NCBI BLAST1 and WU-BLAST, this data
: is P-value. for NCBI BLAST2 it is an Expect value.
=cut
=head2 signif
Synonym for L<max_significance()|max_significance>
=cut
=head2 min_score
Usage : $obj->min_score();
Purpose : Set/Get the Blast score used as screening cutoff.
This is the value of the -score parameter supplied to new().
Hits with scores below this are skipped.
Returns : Integer or scientific notation number.
Argument : Integer or scientific notation number (when setting)
Comments : Screening of significant hits uses the data provided on the
: description line.
=cut
=head2 min_query_length
Usage : $obj->min_query_length();
Purpose : Gets the query sequence length used as screening criteria.
This is the value of the -min_query_len parameter supplied to new().
Hits with sequence length below this are skipped.
Returns : Integer
Argument : n/a
=cut
=head2 best_hit_only
Title : best_hit_only
Usage : print "only getting best hit.\n" if $obj->best_hit_only;
Purpose : Set/Get the indicator for whether or not to process only
: the best BlastHit.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)
=cut
=head2 check_all_hits
Title : check_all_hits
Usage : print "checking all hits.\n" if $obj->check_all_hits;
Purpose : Set/Get the indicator for whether or not to process all hits.
: If false, the parser will stop processing hits after the
: the first non-significance hit or the first hit that fails
: any hit filter.
Returns : Boolean (1 | 0)
Argument : Boolean (1 | 0) (when setting)
=cut
# general private method used to make minimal hits from leftover
# data in the hit table
sub _cleanup_hits {
my ($self, $hits) = @_;
while ( my $v = shift @{ $hits }) {
next unless defined $v;
$self->start_element( { 'Name' => 'Hit' } );
my $id = $v->[2];
my $desc = $v->[3];
$self->element(
{
'Name' => 'Hit_id',
'Data' => $id
}
);
my ($gi, $acc, $version ) = $self->_get_seq_identifiers($id);
$self->element(
{
'Name' => 'Hit_accession',
'Data' => $acc
}
);
if ( defined $v ) {
$self->element(
{
'Name' => 'Hit_signif',
'Data' => $v->[0]
}
);
if (exists $self->{'_wublast'}) {
$self->element(
{
'Name' => 'Hit_score',
'Data' => $v->[1]
}
);
} else {
$self->element(
{
'Name' => 'Hit_bits',
'Data' => $v->[1]
}
);
}
}
$self->element(
{
'Name' => 'Hit_def',
'Data' => $desc
}
);
$self->end_element( { 'Name' => 'Hit' } );
}
}
1;
__END__
Developer Notes
---------------
The following information is added in hopes of increasing the
maintainability of this code. It runs the risk of becoming obsolete as
the code gets updated. As always, double check against the actual
source. If you find any discrepencies, please correct them.
[ This documentation added on 3 Jun 2003. ]
The logic is the brainchild of Jason Stajich, documented by Steve
Chervitz. Jason: please check it over and modify as you see fit.
Question:
Elmo wants to know: How does this module unmarshall data from the input stream?
(i.e., how does information from a raw input file get added to
the correct Bioperl object?)
Answer:
This answer is specific to SearchIO::blast, but may apply to other
SearchIO.pm subclasses as well. The following description gives the
basic idea. The actual processing is a little more complex for
certain types of data (HSP, Report Parameters).
You can think of blast::next_result() as faking a SAX XML parser,
making a non-XML document behave like its XML. The overhead to do this
is quite substantial (~650 lines of code instead of ~80 in
blastxml.pm).
0. First, add a key => value pair for the datum of interest to %MAPPING
Example:
'Foo_bar' => 'Foo-bar',
1. next_result() collects the datum of interest from the input stream,
and calls element().
Example:
$self->element({ 'Name' => 'Foo_bar',
'Data' => $foobar});
2. The element() method is a convenience method that calls start_element(),
characters(), and end_element().
3. start_element() checks to see if the event handler can handle a start_xxx(),
where xxx = the 'Name' parameter passed into element(), and calls start_xxx()
if so. Otherwise, start_element() does not do anything.
Data that will have such an event handler are defined in %MODEMAP.
Typically, there are only handler methods for the main parts of
the search result (e.g., Result, Iteration, Hit, HSP),
which have corresponding Bioperl modules. So in this example,
there was an earlier call such as $self->element({'Name'=>'Foo'})
and the Foo_bar datum is meant to ultimately go into a Foo object.
The start_foo() method in the handler will typically do any
data initialization necessary to prepare for creating a new Foo object.
Example: SearchResultEventBuilder::start_result()
4. characters() takes the value of the 'Data' key from the hashref argument in
the elements() call and saves it in a local data member:
Example:
$self->{'_last_data'} = $data->{'Data'};
5. end_element() is like start_element() in that it does the check for whether
the event handler can handle end_xxx() and if so, calls it, passing in
the data collected from all of the characters() calls that occurred
since the start_xxx() call.
If there isn't any special handler for the data type specified by 'Name',
end_element() will place the data saved by characters() into another
local data member that saves it in a hash with a key defined by %MAPPING.
Example:
$nm = $data->{'Name'};
$self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
In this case, $MAPPING{$nm} is 'Foo-bar'.
end_element() finishes by resetting the local data member used by
characters(). (i.e., $self->{'_last_data'} = '';)
6. When the next_result() method encounters the end of the Foo element in the
input stream. It will invoke $self->end_element({'Name'=>'Foo'}).
end_element() then sends all of the data in the $self->{'_values'} hash.
Note that $self->{'_values'} is cleaned out during start_element(),
keeping it at a resonable size.
In the event handler, the end_foo() method takes the hash from end_element()
and creates a new hash containing the same data, but having keys lacking
the 'Foo' prefix (e.g., 'Foo-bar' becomes '-bar'). The handler's end_foo()
method then creates the Foo object, passing in this new hash as an argument.
Example: SearchResultEventBuilder::end_result()
7. Objects created from the data in the search result are managed by
the event handler which adds them to a ResultI object (using API methods
for that object). The ResultI object gets passed back to
SearchIO::end_element() when it calls end_result().
The ResultI object is then saved in an internal data member of the
SearchIO object, which returns it at the end of next_result()
by calling end_document().
(Technical Note: All objects created by end_xxx() methods in the event
handler are returned to SearchIO::end_element(), but the SearchIO object
only cares about the ResultI objects.)
(Sesame Street aficionados note: This answer was NOT given by Mr. Noodle ;-P)
|