#! /usr/bin/perl # Bug #h80: hmmconvert can't read H2 Nucleic files # # Usage: ./i15-hmmconvert.pl # Example: ./i15-hmmconvert.pl .. .. tmpfoo # # SRE, Tue May 18 13:32:40 2010 [Janelia] # SVN $Id$ BEGIN { $builddir = shift; $srcdir = shift; $tmppfx = shift; } # Verify that we have all the executables we need for the test. if (! -x "$builddir/src/hmmconvert") { die "FAIL: didn't find hmmconvert binary in $builddir/src\n"; } # Create our test files (data embedded in script as functions: see end of file &h2_nt_file("$tmppfx.nt.hmm"); &h2_aa_file("$tmppfx.aa.hmm"); @output = `$builddir/src/hmmconvert $tmppfx.nt.hmm 2>&1`; if ($? != 0) { die "FAIL: hmmconvert of H2 nucleic model failed\n"; } @output = `$builddir/src/hmmconvert $tmppfx.aa.hmm 2>&1`; if ($? != 0) { die "FAIL: hmmconvert of H2 protein model failed\n"; } print "ok\n"; unlink "$tmppfx.nt.hmm"; unlink "$tmppfx.aa.hmm"; exit 0; sub h2_nt_file { my ($hmmfile) = @_; open(HMMFILE, ">$hmmfile") || die "FAIL: couldn't write $hmmfile\n"; print HMMFILE <<"EOF"; HMMER2.0 [2.3.2] NAME ecori LENG 6 ALPH Nucleic RF no CS no MAP yes COM hmmbuild ecori.hmm testsuite/ecori.sto NSEQ 2 DATE Tue May 18 13:30:52 2010 CKSUM 3108 XT -9967 -1 -1000 -1000 -9967 -1 -9967 -1 NULT -1 -9967 NULE 0 0 0 0 HMM A C G T m->m m->i m->d i->m i->i d->m d->d b->m m->e -415 * -2000 1 -585 -585 1000 -585 1 - 0 0 0 0 - -21 -6672 -7714 -894 -1115 -701 -1378 -415 * 2 1000 -585 -585 -585 2 - 0 0 0 0 - -21 -6672 -7714 -894 -1115 -701 -1378 * * 3 1000 -585 -585 -585 3 - 0 0 0 0 - -21 -6672 -7714 -894 -1115 -701 -1378 * * 4 -585 -585 -585 1000 4 - 0 0 0 0 - -21 -6672 -7714 -894 -1115 -701 -1378 * * 5 -585 -585 -585 1000 5 - 0 0 0 0 - -21 -6672 -7714 -894 -1115 -701 -1378 * * 6 -585 1000 -585 -585 6 - * * * * - * * * * * * * * 0 // EOF close HMMFILE; } sub h2_aa_file { my ($hmmfile) = @_; open(HMMFILE, ">$hmmfile") || die "FAIL: couldn't write $hmmfile\n"; print HMMFILE <<"EOF"; HMMER2.0 [2.3.2] NAME test LENG 20 ALPH Amino RF yes CS no MAP yes COM hmmbuild 20aa.hmm testsuite/20aa.sto NSEQ 10 DATE Tue May 18 13:38:05 2010 CKSUM 9020 XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 NULT -4 -8455 NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d b->m m->e -585 * -1585 1 2806 -444 -1270 -1265 -1732 -744 -1182 -1034 -1212 -1545 -1010 -869 -1380 -1102 -1325 -156 -259 -640 -2039 -1721 1 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 -585 * 2 -608 5196 -2368 -2362 -1635 -1253 -1702 -987 -2034 -1540 -1191 -1745 -1831 -1953 -1922 -934 -927 -770 -1855 -1692 2 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 3 -1130 -2063 3441 243 -2502 -1157 -662 -2514 -843 -2578 -2029 -96 -1658 -421 -1434 -970 -1239 -2138 -2388 -1915 3 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 4 -988 -1921 379 3052 -2309 -1196 -495 -2108 -350 -2194 -1612 -103 -1621 -210 -770 -862 -1042 -1799 -2207 -1742 4 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 5 -1602 -1340 -2512 -2455 3740 -2315 -379 -478 -2225 -175 -190 -1874 -2503 -1781 -2079 -1892 -1647 -683 210 1257 5 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 6 -759 -1104 -1314 -1488 -2461 3330 -1563 -2503 -1721 -2645 -2082 -1325 -1776 -1591 -1791 -959 -1094 -1922 -2199 -2280 6 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - 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-33 -6045 -7087 -894 -1115 -701 -1378 * * 12 -637 -1349 -5 -148 -1773 -1078 -624 -1965 -499 -2112 -1514 3456 -1574 -435 -810 -661 -818 -1560 -1900 -1327 12 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 13 -934 -1220 -1352 -1451 -2187 -1314 -1456 -2160 -1488 -2268 -1827 -1359 3760 -1471 -1571 -1129 -1216 -1780 -2050 -2023 13 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 14 -862 -1548 -321 -247 -1672 -1336 -419 -1721 130 -1660 -1161 -427 -1678 3540 -59 -855 -904 -1495 -1728 -1237 14 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 15 -1181 -1614 -1431 -903 -2066 -1632 -446 -1944 559 -1867 -1326 -899 -1873 -156 3432 -1225 -1148 -1717 -1746 -1529 15 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 16 116 -498 -840 -867 -1751 -671 -949 -1625 -916 -1896 -1218 -622 -1304 -824 -1097 2786 -220 -1038 -1992 -1530 16 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 17 -52 -555 -1173 -1112 -1571 -872 -1041 -862 -950 -1353 -866 -843 -1455 -937 -1084 -285 3069 -557 -1898 -1539 17 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 18 -700 -665 -2337 -2135 -873 -1965 -1727 1107 -1863 -105 22 -1851 -2286 -1794 -1920 -1368 -823 2927 -1816 -1362 18 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 19 -1926 -1577 -2416 -2370 192 -2070 -795 -1602 -1882 -1347 -1210 -2018 -2383 -1854 -1777 -2150 -1992 -1643 5696 560 19 x -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -33 -6045 -7087 -894 -1115 -701 -1378 * * 20 -1667 -1473 -2001 -1964 1181 -2210 -25 -1224 -1658 -1018 -871 -1505 -2415 -1423 -1618 -1747 -1692 -1248 501 4149 20 x * * * * * * * * * * * * * * * * * * * * - * * * * * * * * 0 // EOF close HMMFILE; }