// =============================================================== // // // // File : arb_probe.cxx // // Purpose : // // // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // =============================================================== // #include #include #include #include #include #include #include #include #include #include // need to include before test_unit.h #include struct apd_sequence { apd_sequence *next; const char *sequence; }; struct Params { int DESIGNCLIPOUTPUT; int SERVERID; const char *DESIGNNAMES; int DESIGNPROBELEN; int DESIGNMAXPROBELEN; const char *DESIGNSEQUENCE; int MINTEMP; int MAXTEMP; int MINGC; int MAXGC; int MAXBOND; int MINPOS; int MAXPOS; int MISHIT; int MINTARGETS; const char *SEQUENCE; int MISMATCHES; int ACCEPTN; int LIMITN; int MAXRESULT; int ALSO_REVCOMPL; int WEIGHTED; apd_sequence *sequence; int ITERATE; int ITERATE_AMOUNT; int ITERATE_READABLE; const char *ITERATE_SEPARATOR; const char *ITERATE_TU; const char *DUMP; }; struct gl_struct { aisc_com *link; T_PT_MAIN com; T_PT_LOCS locs; int pd_design_id; gl_struct() : link(NULp), pd_design_id(0) {} }; static Params P; static gl_struct pd_gl; static int init_local_com_struct() { const char *user = GB_getenvUSER(); if (aisc_create(pd_gl.link, PT_MAIN, pd_gl.com, MAIN_LOCS, PT_LOCS, pd_gl.locs, LOCS_USER, user, NULp)) { return 1; } return 0; } class PTserverConnection { static int count; bool need_close; public: PTserverConnection(ARB_ERROR& error) : need_close(false) { if (count) { error = "Only 1 PTserverConnection allowed"; } else { ++count; GB_ERROR lookerr = NULp; const char *servername = arb_look_and_start_ptserver(AISC_MAGIC_NUMBER, P.SERVERID, lookerr); if (servername) { GB_ERROR openerr = NULp; pd_gl.link = aisc_open(servername, pd_gl.com, AISC_MAGIC_NUMBER, &openerr); if (openerr) { error = openerr; } else { if (!pd_gl.link) { error = "Cannot contact PT_SERVER [1]"; } else if (init_local_com_struct()) { error = "Cannot contact PT_SERVER [2]"; } else { need_close = true; } } } else { error = lookerr; } } } ~PTserverConnection() { if (need_close) { aisc_close(pd_gl.link, pd_gl.com); pd_gl.link = NULp; } --count; } }; int PTserverConnection::count = 0; static char *AP_dump_index_event(ARB_ERROR& error) { PTserverConnection contact(error); char *result = NULp; if (!error) { aisc_put(pd_gl.link, PT_MAIN, pd_gl.com, MAIN_DUMP_NAME, P.DUMP, NULp); if (aisc_get(pd_gl.link, PT_MAIN, pd_gl.com, MAIN_DUMP_INDEX, &result, NULp)) { error = "Connection to PT_SERVER lost (1)"; } else { result = ARB_strdup("ok"); } } return result; } static char *AP_probe_iterate_event(ARB_ERROR& error) { PTserverConnection contact(error); char *result = NULp; if (!error) { T_PT_PEP pep; int length = P.ITERATE; if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs, LOCS_PROBE_FIND_CONFIG, PT_PEP, pep, PEP_PLENGTH, (long)length, PEP_RESTART, (long)1, PEP_READABLE, (long)P.ITERATE_READABLE, PEP_TU, (long)P.ITERATE_TU[0], PEP_SEPARATOR, (long)P.ITERATE_SEPARATOR[0], NULp)) { error = "Connection to PT_SERVER lost (1)"; } if (!error) { int amount = P.ITERATE_AMOUNT; int amount_per_call = AISC_MAX_STRING_LEN/(length+2); GBS_strstruct out(50000); bool first = true; while (amount && !error) { int this_amount = std::min(amount, amount_per_call); aisc_put(pd_gl.link, PT_PEP, pep, PEP_NUMGET, (long)this_amount, PEP_FIND_PROBES, (long)0, NULp); char *pep_result = NULp; if (aisc_get(pd_gl.link, PT_PEP, pep, PEP_RESULT, &pep_result, NULp)) { error = "Connection to PT_SERVER lost (2)"; } if (!error) { if (pep_result[0]) { if (first) first = false; else out.put(P.ITERATE_SEPARATOR[0]); out.cat(pep_result); amount -= this_amount; } else { amount = 0; // terminate loop } } free(pep_result); } if (!error) { result = out.release(); } } } if (error) freenull(result); return result; } static char *AP_probe_design_event(ARB_ERROR& error) { PTserverConnection contact(error); if (!error) { bytestring bs; bs.data = (char*)(P.DESIGNNAMES); bs.size = strlen(bs.data)+1; T_PT_PDC pdc; if (aisc_create(pd_gl.link, PT_LOCS, pd_gl.locs, LOCS_PROBE_DESIGN_CONFIG, PT_PDC, pdc, PDC_MIN_PROBELEN, (long)P.DESIGNPROBELEN, PDC_MAX_PROBELEN, (long)P.DESIGNMAXPROBELEN, PDC_MINTEMP, (double)P.MINTEMP, PDC_MAXTEMP, (double)P.MAXTEMP, PDC_MINGC, (double)P.MINGC/100.0, PDC_MAXGC, (double)P.MAXGC/100.0, PDC_MAXBOND, (double)P.MAXBOND, PDC_MIN_ECOLIPOS, (long)P.MINPOS, PDC_MAX_ECOLIPOS, (long)P.MAXPOS, PDC_MISHIT, (long)P.MISHIT, PDC_MINTARGETS, (double)P.MINTARGETS/100.0, PDC_CLIPRESULT, (long)P.DESIGNCLIPOUTPUT, NULp)) { error = "Connection to PT_SERVER lost (1)"; } if (!error) { for (apd_sequence *s = P.sequence; s; ) { apd_sequence *next = s->next; bytestring bs_seq; T_PT_SEQUENCE pts; bs_seq.data = (char*)s->sequence; bs_seq.size = strlen(bs_seq.data)+1; aisc_create(pd_gl.link, PT_PDC, pdc, PDC_SEQUENCE, PT_SEQUENCE, pts, SEQUENCE_SEQUENCE, &bs_seq, NULp); delete s; s = next; } aisc_put(pd_gl.link, PT_PDC, pdc, PDC_NAMES, &bs, PDC_GO, (long)0, NULp); { char *locs_error = NULp; if (aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs, LOCS_ERROR, &locs_error, NULp)) { error = "Connection to PT_SERVER lost (2)"; } else { if (*locs_error) error = GBS_static_string(locs_error); free(locs_error); } } if (!error) { T_PT_TPROBE tprobe; aisc_get(pd_gl.link, PT_PDC, pdc, PDC_TPROBE, tprobe.as_result_param(), NULp); GBS_strstruct outstr(1000); if (tprobe.exists()) { char *match_info = NULp; aisc_get(pd_gl.link, PT_PDC, pdc, PDC_INFO_HEADER, &match_info, NULp); outstr.cat(match_info); outstr.put('\n'); free(match_info); } while (tprobe.exists()) { char *match_info = NULp; if (aisc_get(pd_gl.link, PT_TPROBE, tprobe, TPROBE_NEXT, tprobe.as_result_param(), TPROBE_INFO, &match_info, NULp)) break; outstr.cat(match_info); outstr.put('\n'); free(match_info); } return outstr.release(); } } } return NULp; } static char *AP_probe_match_event(ARB_ERROR& error) { PTserverConnection contact(error); if (!error && aisc_nput(pd_gl.link, PT_LOCS, pd_gl.locs, LOCS_MATCH_ALSO_REVCOMP, (long)P.ALSO_REVCOMPL, LOCS_COMPLEMENT_FIRST, (long)0, // (use sequence passed below as is. do not complement it.) LOCS_MATCH_SORT_BY, (long)P.WEIGHTED, LOCS_MATCH_MAX_MISMATCHES, (long)P.MISMATCHES, LOCS_MATCH_N_ACCEPT, (long)P.ACCEPTN, LOCS_MATCH_N_LIMIT, (long)P.LIMITN, LOCS_MATCH_MAX_HITS, (long)P.MAXRESULT, LOCS_SEARCHMATCH, P.SEQUENCE, NULp)) { error = "Connection to PT_SERVER lost (1)"; } if (!error) { bytestring bs; bs.data = NULp; { char *locs_error = NULp; T_PT_MATCHLIST match_list; long match_list_cnt; aisc_get(pd_gl.link, PT_LOCS, pd_gl.locs, LOCS_MATCH_LIST, match_list.as_result_param(), LOCS_MATCH_LIST_CNT, &match_list_cnt, LOCS_MATCH_STRING, &bs, LOCS_ERROR, &locs_error, NULp); if (*locs_error) error = GBS_static_string(locs_error); free(locs_error); } if (!error) return bs.data; // freed by caller free(bs.data); } return NULp; } static int pargc; static const char **pargv = NULp; static bool showhelp; static bool outOfRange; static int getInt(const char *param, int val, int min, int max, const char *description) { if (showhelp) { printf(" %s=%i [%i .. ", param, val, min); if (max != INT_MAX) printf("%i", max); printf("] %s\n", description); return 0; } int i; const char *s = NULp; arb_assert(min<=val && val<=max); // wrong default value arb_assert(pargc >= 1); // otherwise s stays 0 for (i=1; i= 1); // otherwise s stays 0 for (i=1; inext = P.sequence; P.sequence = s; s->sequence = P.DESIGNSEQUENCE; P.DESIGNSEQUENCE = NULp; } P.DESIGNPROBELEN = getInt("designprobelength", 18, 2, 100, "(min.) length of probe"); P.DESIGNMAXPROBELEN = getInt("designmaxprobelength", -1, -1, 100, "max. length of probe (if specified)"); P.MINTEMP = getInt("designmintemp", 0, 0, 400, "Minimum melting temperature of probe"); P.MAXTEMP = getInt("designmaxtemp", 400, 0, 400, "Maximum melting temperature of probe"); P.MINGC = getInt("designmingc", 30, 0, 100, "Minimum gc content"); P.MAXGC = getInt("designmaxgc", 80, 0, 100, "Maximum gc content"); P.MAXBOND = getInt("designmaxbond", 0, 0, 10, "Not implemented"); P.MINPOS = getInt("designminpos", -1, -1, INT_MAX, "Minimum ecoli position (-1=none)"); P.MAXPOS = getInt("designmaxpos", -1, -1, INT_MAX, "Maximum ecoli position (-1=none)"); P.MISHIT = getInt("designmishit", 0, 0, 10000, "Number of allowed hits outside the selected group"); P.MINTARGETS = getInt("designmintargets", 50, 0, 100, "Minimum percentage of hits within the selected species"); P.SEQUENCE = getString("matchsequence", "agtagtagt", "The sequence to search for"); P.MISMATCHES = getInt("matchmismatches", 0, 0, INT_MAX, "Maximum Number of allowed mismatches"); P.ALSO_REVCOMPL = getInt("matchAlsoRevcomp", 0, 0, 1, "Also match reverse-complemented probe"); P.WEIGHTED = getInt("matchweighted", 0, 0, 1, "Use weighted mismatches"); P.ACCEPTN = getInt("matchacceptN", 1, 0, INT_MAX, "Amount of N-matches not counted as mismatch"); P.LIMITN = getInt("matchlimitN", 4, 0, INT_MAX, "Limit for N-matches. If reached N-matches are mismatches"); P.MAXRESULT = getInt("matchmaxresults", 1000000, 0, INT_MAX, "Max. number of matches reported (0=unlimited)"); P.ITERATE = getInt("iterate", 0, 0, 20, "Iterate over probes of given length"); P.ITERATE_AMOUNT = getInt("iterate_amount", 100, 1, INT_MAX, "Number of results per answer"); P.ITERATE_READABLE = getInt("iterate_readable", 1, 0, 1, "readable results"); P.ITERATE_TU = getString("iterate_tu", "T", "use T or U in readable result"); P.ITERATE_SEPARATOR = getString("iterate_separator", ";", "Number of results per answer"); P.DUMP = getString("dump", "", "dump ptserver index to file (may be huge!)"); if (pargc>1) { printf("Unknown (or duplicate) parameter %s\n", pargv[1]); return false; } if (outOfRange) { puts("Not all parameters were inside allowed range\n"); return false; } return !showhelp; } // -------------------------------------------------------------------------------- #ifdef UNIT_TESTS #ifndef TEST_UNIT_H #include #endif void TEST_BASIC_parseCommandLine() { { const char *args[] = { NULp, "serverid=0"}; TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args)); // test default values here TEST_EXPECT_EQUAL(P.ACCEPTN, 1); TEST_EXPECT_EQUAL(P.LIMITN, 4); TEST_EXPECT_EQUAL(P.MISMATCHES, 0); TEST_EXPECT_EQUAL(P.MAXRESULT, 1000000); } { const char *args[] = {NULp, "serverid=4", "matchmismatches=2"}; TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args)); TEST_EXPECT_EQUAL(P.SERVERID, 4); TEST_EXPECT_EQUAL(P.MISMATCHES, 2); TEST_EXPECT_EQUAL(args[1], "serverid=4"); // check array args was not modified } { const char *args[] = { NULp, "matchacceptN=0", "matchlimitN=5"}; TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args)); TEST_EXPECT_EQUAL(P.ACCEPTN, 0); TEST_EXPECT_EQUAL(P.LIMITN, 5); } { const char *args[] = { NULp, "matchmaxresults=100"}; TEST_EXPECT(parseCommandLine(ARRAY_ELEMS(args), args)); TEST_EXPECT_EQUAL(P.MAXRESULT, 100); } } #endif // UNIT_TESTS // -------------------------------------------------------------------------------- static char *execute(ARB_ERROR& error) { char *answer; if (*P.DESIGNNAMES || P.sequence) { answer = AP_probe_design_event(error); } else if (P.ITERATE>0) { answer = AP_probe_iterate_event(error); } else if (P.DUMP[0]) { answer = AP_dump_index_event(error); } else { answer = AP_probe_match_event(error); } pd_gl.locs.clear(); return answer; } int ARB_main(int argc, char *argv[]) { bool ok = parseCommandLine(argc, argv); if (ok) { ARB_ERROR error; char *answer = execute(error); arb_assert(contradicted(answer, error)); if (!answer) { fprintf(stderr, "arb_probe: Failed to process your request\n" " Reason: %s", error.deliver()); ok = false; } else { fputs(answer, stdout); free(answer); error.expect_no_error(); } } return ok ? EXIT_SUCCESS : EXIT_FAILURE; } // -------------------------------------------------------------------------------- #ifdef UNIT_TESTS #ifndef TEST_UNIT_H #include #endif static int test_setup(bool use_gene_ptserver) { static bool setup[2] = { false, false }; if (!setup[use_gene_ptserver]) { TEST_SETUP_GLOBAL_ENVIRONMENT(use_gene_ptserver ? "ptserver_gene" : "ptserver"); // first call will recreate the test pt-server setup[use_gene_ptserver] = true; } return use_gene_ptserver ? TEST_GENESERVER_ID : TEST_SERVER_ID; } // ---------------------------------- // test probe design / match #define TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv) \ int serverid = test_setup(use_gene_ptserver); \ TEST_EXPECT_EQUAL(true, parseCommandLine(fake_argc, fake_argv)); \ TEST_EXPECT((serverid == TEST_SERVER_ID)||(serverid == TEST_GENESERVER_ID)); \ P.SERVERID = serverid; \ ARB_ERROR error; \ char *answer = execute(error) #define TEST_ARB_PROBE__REPORTS_ERROR(fake_argc,fake_argv,expected_error) \ TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \ free(answer); \ TEST_EXPECT_ERROR_CONTAINS(error.deliver(), expected_error) #define TEST_ARB_PROBE__REPORTS_ERROR__BROKEN(fake_argc,fake_argv,expected_error) \ TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \ free(answer); \ TEST_EXPECT_ANY_ERROR(error.preserve()); \ TEST_EXPECT_ERROR_CONTAINS__BROKEN(error.deliver(), expected_error) #define TEST_RUN_ARB_PROBE(fake_argc,fake_argv) \ TEST_RUN_ARB_PROBE__INT(fake_argc,fake_argv); \ TEST_EXPECT_NO_ERROR(error.deliver()) #define TEST_ARB_PROBE(fake_argc,fake_argv,expected) do { \ TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \ TEST_EXPECT_EQUAL(answer, expected); \ free(answer); \ } while(0) #define TEST_ARB_PROBE__BROKEN(fake_argc,fake_argv,expected) do { \ TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \ TEST_EXPECT_EQUAL__BROKEN(answer, expected); \ free(answer); \ } while(0) #define TEST_ARB_PROBE_FILT(fake_argc,fake_argv,filter,expected) do { \ TEST_RUN_ARB_PROBE(fake_argc,fake_argv); \ char *filtered = filter(answer); \ TEST_EXPECT_EQUAL(filtered, expected); \ free(filtered); \ free(answer); \ } while(0) typedef const char *CCP; void TEST_SLOW_match_geneprobe() { // test here runs versus database ../UNIT_TESTER/run/TEST_gpt_src.arb bool use_gene_ptserver = true; { const char *arguments[] = { "prgnamefake", "matchsequence=NNUCNN", "matchacceptN=4", "matchlimitN=5", }; CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NNUCNN'\1" "genome2\1" " genome2 gene3 0 4 2.6 2 1 0 .........-UU==GG-UUGAUC.\1" "genome2\1" " genome2 joined1 0 4 2.6 2 1 0 .........-UU==GG-UUGAUCCUG\1" "genome2\1" " genome2 gene1 0 4 2.6 2 2 0 ........A-UU==GG-U.\1" "genome2\1" " genome2 intergene_19_65 0 4 2.7 31 12 0 GGUUACUGC-AU==GG-UGUUCGCCU\1" "genome1\1" " genome1 intergene_17_65 0 4 2.7 31 14 0 GGUUACUGC-UA==GG-UGUUCGCCU\1" "genome2\1" " genome2 intergene_19_65 0 4 2.7 38 19 0 GCAUUCGGU-GU==GC-CUAAGCACU\1" "genome1\1" " genome1 intergene_17_65 0 4 2.7 38 21 0 GCUAUCGGU-GU==GC-CUAAGCCAU\1" "genome2\1" " genome2 gene3 0 4 2.9 10 9 0 .UUUCGGUU-GA==..-\1" "genome2\1" " genome2 intergene_19_65 0 4 3.1 56 37 0 AGCACUGCG-AG==AU-AUGUA.\1" "genome1\1" " genome1 intergene_17_65 0 4 3.1 56 39 0 AGCCAUGCG-AG==AU-AUGUA.\1" "genome1\1" " genome1 gene2 0 4 3.1 10 2 0 ........U-GA==CU-GC.\1" "genome2\1" " genome2 gene2 0 4 3.1 10 4 0 ......GUU-GA==CU-GCCA.\1" "genome1\1" " genome1 joined1 0 4 3.1 10 7 0 ...CUGGUU-GA==CU-GC.\1" "genome2\1" " genome2 joined1 0 4 3.1 10 9 0 .UUUCGGUU-GA==CU-GCCA.\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); } { const char *arguments[] = { "prgnamefake", "matchsequence=NGGUUN", "matchacceptN=2", "matchlimitN=3", }; CCP expectd = " organism genename------- mis N_mis wmis pos gpos rev 'NGGUUN'\1" "genome1\1" " genome1 gene3 0 2 1.3 5 2 0 ........C-U====G-A.\1" "genome1\1" " genome1 joined1 0 2 1.3 5 2 0 ........C-U====G-AUCCUGC.\1" "genome2\1" " genome2 gene3 0 2 1.4 5 4 0 ......UUU-C====G-AUC.\1" "genome2\1" " genome2 joined1 0 2 1.4 5 4 0 ......UUU-C====G-AUCCUGCCA\1" "genome2\1" " genome2 intergene_19_65 0 2 1.8 21 2 0 ........G-A====A-CUGCAUUCG\1" "genome1\1" " genome1 intergene_17_65 0 2 1.8 21 4 0 ......CAG-A====A-CUGCUAUCG\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); } { const char *arguments[] = { "prgnamefake", "matchsequence=UGAUCCU", // exists in data }; CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UGAUCCU'\1" "genome1\1" " genome1 gene2 0 0 0.0 9 1 0 .........-=======-GC.\1" "genome2\1" " genome2 gene2 0 0 0.0 9 3 0 .......GU-=======-GCCA.\1" "genome1\1" " genome1 joined1 0 0 0.0 9 6 0 ....CUGGU-=======-GC.\1" "genome2\1" " genome2 joined1 0 0 0.0 9 8 0 ..UUUCGGU-=======-GCCA.\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'joined1' (of both genomes)] } { const char *arguments[] = { "prgnamefake", "matchsequence=GAUCCU", }; CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'GAUCCU'\1" "genome1\1" " genome1 gene2 0 0 0.0 10 2 0 ........U-======-GC.\1" "genome2\1" " genome2 gene2 0 0 0.0 10 4 0 ......GUU-======-GCCA.\1" "genome1\1" " genome1 joined1 0 0 0.0 10 7 0 ...CUGGUU-======-GC.\1" "genome2\1" " genome2 joined1 0 0 0.0 10 9 0 .UUUCGGUU-======-GCCA.\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports as much hits as previous test; expected cause probe is part of above probe] } { const char *arguments[] = { "prgnamefake", "matchsequence=UUUCGG", // exists only in genome2 }; CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUUCGG'\1" "genome2\1" " genome2 gene3 0 0 0.0 2 1 0 .........-======-UUGAUC.\1" "genome2\1" " genome2 joined1 0 0 0.0 2 1 0 .........-======-UUGAUCCUG\1" "genome2\1" " genome2 gene1 0 0 0.0 2 2 0 ........A-======-U.\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in genome2/gene1] } { const char *arguments[] = { "prgnamefake", "matchsequence=AUCCUG", }; CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'AUCCUG'\1" "genome1\1" " genome1 gene2 0 0 0.0 11 3 0 .......UG-======-C.\1" "genome2\1" " genome2 gene2 0 0 0.0 11 5 0 .....GUUG-======-CCA.\1" "genome1\1" " genome1 joined1 0 0 0.0 11 8 0 ..CUGGUUG-======-C.\1" "genome2\1" " genome2 joined1 0 0 0.0 11 10 0 UUUCGGUUG-======-CCA.\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hits in 'gene2' and 'joined1' of both genomes] } { const char *arguments[] = { "prgnamefake", "matchsequence=UUGAUCCUGC", }; CCP expectd = " organism genename mis N_mis wmis pos gpos rev 'UUGAUCCUGC'\1" "genome2\1" " genome2 gene2 0 0 0.0 8 2 0 ........G-==========-CA.\1" "genome1\1" " genome1 joined1 0 0 0.0 8 5 0 .....CUGG-==========-.\1" "genome2\1" " genome2 joined1 0 0 0.0 8 7 0 ...UUUCGG-==========-CA.\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd); // [fixed: now reports hit in 'genome2/joined1'] } } __ATTR__REDUCED_OPTIMIZE void TEST_SLOW_match_probe() { // test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb bool use_gene_ptserver = false; { const char *arguments[] = { "prgnamefake", "matchsequence=UAUCGGAGAGUUUGA", }; CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UAUCGGAGAGUUUGA'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 3 2 0 .......UU-===============-UCAAGUCGA\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } // ---------------------------------------------------------------------------- // match with old(=default) N-mismatch-behavior (accepting 1 N-match) { const char *arguments[] = { "prgnamefake", "matchsequence=CANCUCCUUUC", // contains 1 N NULp // matchmismatches }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"; // only N-mismatch accepted CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1" "ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1" "PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1" "DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1" "VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1" "ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1" "PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1" "DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1" "VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1" "PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1" "DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1" "FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1" "HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1" "CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1"; CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1" "ClfPerfr\1" " ClfPerfr 1 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1" "PbcAcet2\1" " PbcAcet2 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "PbrPropi\1" " PbrPropi 1 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "Stsssola\1" " Stsssola 1 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1" "DcdNodos\1" " DcdNodos 1 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1" "VbrFurni\1" " VbrFurni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VblVulni\1" " VblVulni 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VbhChole\1" " VbhChole 1 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "AclPleur\1" " AclPleur 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1" "PtVVVulg\1" " PtVVVulg 2 2 2.7 176 162 0 CGGUUGGAU-==C======A.-\1" "DlcTolu2\1" " DlcTolu2 2 3 2.3 176 162 0 CGGCUGGAU-==C======NN-N.\1" "FrhhPhil\1" " FrhhPhil 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1" "HllHalod\1" " HllHalod 2 3 2.3 176 162 0 CGGCUGGAU-==C======..-\1" "CPPParap\1" " CPPParap 2 3 2.3 177 163 0 CGGNUGGAU-==C======..-\1" "VblVulni\1" " VblVulni 3 1 3.6 49 44 0 AGCACAGAG-a=A==uG====-UCGGGUGGC\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3); } { const char *arguments[] = { "prgnamefake", "matchsequence=UCACCUCCUUUC", // contains no N NULp // matchmismatches }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"; CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1" "PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1" "DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1" "FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1" "HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1" "CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 0 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 0 1 0.7 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 0 1 0.7 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 0 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "AclPleur\1" " AclPleur 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1" "PtVVVulg\1" " PtVVVulg 1 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1" "DlcTolu2\1" " DlcTolu2 1 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1" "FrhhPhil\1" " FrhhPhil 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1" "HllHalod\1" " HllHalod 1 2 1.4 175 161 0 GCGGCUGGA-==========..-\1" "CPPParap\1" " CPPParap 1 2 1.4 176 162 0 GCGGNUGGA-==========..-\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1" "LgtLytic\1" " LgtLytic 2 3 2.1 175 161 0 GCGGCUGGA-=========N..-\1" "PslFlave\1" " PslFlave 2 3 2.1 175 161 0 GCGGCUGGA-=========...-\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); } { const char *arguments[] = { "prgnamefake", "matchsequence=UCACCUCCUUUC", // contains no N NULp, // matchmismatches "matchweighted=1", // use weighted mismatches }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1"; CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1" "FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1" "HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1" "CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1" "AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1" "PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1" "LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1" "PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1" "ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 0 1 0.2 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 0 1 0.2 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 0 1 0.2 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 0 1 0.2 175 161 0 GGCGCUGGA-===========.-\1" "DlcTolu2\1" " DlcTolu2 1 2 0.6 175 161 0 GCGGCUGGA-==========NN-N.\1" "FrhhPhil\1" " FrhhPhil 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1" "HllHalod\1" " HllHalod 1 2 0.6 175 161 0 GCGGCUGGA-==========..-\1" "CPPParap\1" " CPPParap 1 2 0.6 176 162 0 GCGGNUGGA-==========..-\1" "AclPleur\1" " AclPleur 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1" "PtVVVulg\1" " PtVVVulg 1 1 0.9 175 161 0 GCGGUUGGA-==========A.-\1" "LgtLytic\1" " LgtLytic 2 3 1.3 175 161 0 GCGGCUGGA-=========N..-\1" "PslFlave\1" " PslFlave 2 3 1.3 175 161 0 GCGGCUGGA-=========...-\1" "ClfPerfr\1" " ClfPerfr 2 0 1.3 175 161 0 AAGAUUAAU-A=C=========-U.\1" "AclPleur\1" " AclPleur 5 0 2.4 50 45 0 GAAGGGAGC-=ug=u=u====G-CCGACGAGU\1" "PtVVVulg\1" " PtVVVulg 5 0 2.4 50 45 0 GGAGAAAGC-=ug=u=u===g=-UGACGAGCG\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); } // ---------------------------------------------- // do not accept any N-matches as match { const char *arguments[] = { "prgnamefake", "matchsequence=CANCUCCUUUC", // contains 1 N NULp, // matchmismatches "matchacceptN=0", }; CCP expectd0 = ""; // nothing matches CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 1 1 0.9 176 162 0 CGGCUGGAU-==C========-U.\1" "ClfPerfr\1" " ClfPerfr 2 1 2.0 176 162 0 AGAUUAAUA-=CC========-U.\1" "PbcAcet2\1" " PbcAcet2 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "PbrPropi\1" " PbrPropi 2 2 1.6 176 162 0 CGGCUGGAU-==C=======N-N.\1" "Stsssola\1" " Stsssola 2 2 1.6 176 162 0 CGGCUGGAU-==C=======.-\1" "DcdNodos\1" " DcdNodos 2 2 1.6 176 162 0 CGGUUGGAU-==C=======.-\1" "VbrFurni\1" " VbrFurni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VblVulni\1" " VblVulni 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1" "VbhChole\1" " VbhChole 2 2 1.6 176 162 0 GCGCUGGAU-==C=======.-\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); } { const char *arguments[] = { "prgnamefake", "matchsequence=UUUCUUU", // contains no N NULp, // matchmismatches "matchacceptN=0", }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1" "AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1"; CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1" "AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1" "AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1" "PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1" "PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1" "ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UUUCUUU'\1" "AclPleur\1" " AclPleur 0 0 0.0 54 49 0 GGAGCUUGC-=======-GCCGACGAG\1" "AclPleur\1" " AclPleur 1 0 0.6 50 45 0 GAAGGGAGC-==g====-CUUUGCCGA\1" "PtVVVulg\1" " PtVVVulg 1 0 0.6 50 45 0 GGAGAAAGC-==g====-CUUGCUGAC\1" "PtVVVulg\1" " PtVVVulg 1 0 0.6 54 49 0 AAAGCUUGC-======g-CUGACGAGC\1" "ClfPerfr\1" " ClfPerfr 1 0 1.1 49 44 0 GCGAUGAAG-====C==-CGGGAAACG\1" "DlcTolu2\1" " DlcTolu2 2 0 1.2 47 42 0 AGAAAGGGA-==g===g-CAAUCCUGA\1" "ClnCorin\1" " ClnCorin 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAAUGG\1" "CPPParap\1" " CPPParap 2 0 1.7 48 43 0 AGCGAUGAA-g===C==-CGGGAACGG\1" "HllHalod\1" " HllHalod 2 0 1.7 49 44 0 GAUGGAAGC-==g===C-CAGGCGUCG\1" "DcdNodos\1" " DcdNodos 2 0 1.7 50 45 0 UUAUGUAGC-==g==A=-GUAACCUAG\1" "VbhChole\1" " VbhChole 2 0 1.7 55 50 0 GAGGAACUU-g===C==-GGGUGGCGA\1" "VbrFurni\1" " VbrFurni 2 0 1.7 62 57 0 UUCGGGGGA-===G==g-GGCGGCGAG\1" "VblVulni\1" " VblVulni 2 0 1.7 62 57 0 AGAAACUUG-=====Cg-GGUGGCGAG\1" "VbhChole\1" " VbhChole 2 0 1.7 62 57 0 AGGAACUUG-==C===g-GGUGGCGAG\1" "ClnCorin\1" " ClnCorin 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAAUGGA\1" "CltBotul\1" " CltBotul 2 0 2.2 49 44 0 GCGAUGAAG-C=====C-GGAAGUGGA\1" "CPPParap\1" " CPPParap 2 0 2.2 49 44 0 GCGAUGAAG-==C===C-GGGAACGGA\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 50 45 0 CGAUGAAGU-==C===C-GGGAAACGG\1" "VblVulni\1" " VblVulni 2 0 2.2 52 47 0 ACAGAGAAA-C==G===-CUCGGGUGG\1" "BcSSSS00\1" " BcSSSS00 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-CU.\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 179 165 0 UUAAUACCC-C=C====-CU.\1" "PbcAcet2\1" " PbcAcet2 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1" "PbrPropi\1" " PbrPropi 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-NN.\1" "Stsssola\1" " Stsssola 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1" "DcdNodos\1" " DcdNodos 2 0 2.2 179 165 0 UUGGAUCAC-C=C====-.\1" "VbrFurni\1" " VbrFurni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1" "VblVulni\1" " VblVulni 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1" "VbhChole\1" " VbhChole 2 0 2.2 179 165 0 CUGGAUCAC-C=C====-.\1" "BcSSSS00\1" " BcSSSS00 2 2 1.4 183 169 0 AUCACCUCC-=====..-\1" "ClfPerfr\1" " ClfPerfr 2 2 1.4 183 169 0 UACCCCUCC-=====..-\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); } { const char *arguments[] = { "prgnamefake", "matchsequence=UCACCUCCUUUC", // contains no N NULp, // matchmismatches "matchacceptN=0", }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" ""; CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-============-U.\1" "PbcAcet2\1" " PbcAcet2 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "PbrPropi\1" " PbrPropi 1 1 0.7 175 161 0 GCGGCUGGA-===========N-N.\1" "Stsssola\1" " Stsssola 1 1 0.7 175 161 0 GCGGCUGGA-===========.-\1" "DcdNodos\1" " DcdNodos 1 1 0.7 175 161 0 GCGGUUGGA-===========.-\1" "VbrFurni\1" " VbrFurni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VblVulni\1" " VblVulni 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "VbhChole\1" " VbhChole 1 1 0.7 175 161 0 GGCGCUGGA-===========.-\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C=========-U.\1" "AclPleur\1" " AclPleur 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1" "PtVVVulg\1" " PtVVVulg 2 1 1.8 175 161 0 GCGGUUGGA-==========A.-\1" "DlcTolu2\1" " DlcTolu2 2 2 1.4 175 161 0 GCGGCUGGA-==========NN-N.\1" "FrhhPhil\1" " FrhhPhil 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1" "HllHalod\1" " HllHalod 2 2 1.4 175 161 0 GCGGCUGGA-==========..-\1" "CPPParap\1" " CPPParap 2 2 1.4 176 162 0 GCGGNUGGA-==========..-\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); } { const char *arguments[] = { "prgnamefake", "matchsequence=UCACCUCCUUUCU", // contains no N NULp, // matchmismatches "matchacceptN=0", }; CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1" "PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1" "DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1" "VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1"; CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1" "PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1" "DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1" "VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1" "PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1" "DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1" "FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1" "HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1" "CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1"; CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1" "PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1" "DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1" "VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1" "PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1" "DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1" "FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1" "HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1" "CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1" "LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1" "PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1"; CCP expectd5 = " name---- fullname mis N_mis wmis pos ecoli rev 'UCACCUCCUUUCU'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 175 161 0 GCGGCUGGA-=============-.\1" "ClfPerfr\1" " ClfPerfr 2 0 2.2 175 161 0 AAGAUUAAU-A=C==========-.\1" "PbcAcet2\1" " PbcAcet2 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "PbrPropi\1" " PbrPropi 2 2 1.4 175 161 0 GCGGCUGGA-===========NN-.\1" "Stsssola\1" " Stsssola 2 2 1.4 175 161 0 GCGGCUGGA-===========..-\1" "DcdNodos\1" " DcdNodos 2 2 1.4 175 161 0 GCGGUUGGA-===========..-\1" "VbrFurni\1" " VbrFurni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VblVulni\1" " VblVulni 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "VbhChole\1" " VbhChole 2 2 1.4 175 161 0 GGCGCUGGA-===========..-\1" "AclPleur\1" " AclPleur 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1" "PtVVVulg\1" " PtVVVulg 3 2 2.5 175 161 0 GCGGUUGGA-==========A..-\1" "DlcTolu2\1" " DlcTolu2 3 3 2.1 175 161 0 GCGGCUGGA-==========NNN-.\1" "FrhhPhil\1" " FrhhPhil 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1" "HllHalod\1" " HllHalod 3 3 2.1 175 161 0 GCGGCUGGA-==========...-\1" "CPPParap\1" " CPPParap 3 3 2.1 176 162 0 GCGGNUGGA-==========...-\1" "LgtLytic\1" " LgtLytic 4 4 2.8 175 161 0 GCGGCUGGA-=========N...-\1" "PslFlave\1" " PslFlave 4 4 2.8 175 161 0 GCGGCUGGA-=========....-\1" "PtVVVulg\1" " PtVVVulg 5 0 2.6 50 45 0 GGAGAAAGC-=ug=u=u===g==-GACGAGCGG\1" "AclPleur\1" " AclPleur 5 0 3.5 46 41 0 ACGGGAAGG-gag=u=G======-UUGCCGACG\1" "PtVVVulg\1" " PtVVVulg 5 0 4.0 45 40 0 ...AGGAGA-Aag=u=G======-UGCUGACGA\1" "VblVulni\1" " VblVulni 5 0 4.3 48 43 0 CAGCACAGA-ga=a==uG=====-CGGGUGGCG\1"; arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3); arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4); arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd5); } // ---------------------------------- // accept several N-matches { const char *arguments[] = { "prgnamefake", "matchsequence=CANCUCCUUNC", // contains 2 N NULp, // matchmismatches "matchacceptN=2", "matchlimitN=4", }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1" "BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1"; CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1" "BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1" "ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1" "DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1" "FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1" "HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1" "CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1" "PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1" "PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1" "Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1" "DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1" "VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1" "VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1" "VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1" "AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1" "PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCUCCUUNC'\1" "BcSSSS00\1" " BcSSSS00 0 2 1.7 176 162 0 CGGCUGGAU-==C======U=-U.\1" "ClfPerfr\1" " ClfPerfr 1 2 2.8 176 162 0 AGAUUAAUA-=CC======U=-U.\1" "DlcTolu2\1" " DlcTolu2 1 3 2.4 176 162 0 CGGCUGGAU-==C=======N-N.\1" "FrhhPhil\1" " FrhhPhil 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1" "HllHalod\1" " HllHalod 1 3 2.4 176 162 0 CGGCUGGAU-==C======..-\1" "CPPParap\1" " CPPParap 1 3 2.4 177 163 0 CGGNUGGAU-==C======..-\1" "PbcAcet2\1" " PbcAcet2 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1" "PbrPropi\1" " PbrPropi 1 3 2.4 176 162 0 CGGCUGGAU-==C======UN-N.\1" "Stsssola\1" " Stsssola 1 3 2.4 176 162 0 CGGCUGGAU-==C======U.-\1" "DcdNodos\1" " DcdNodos 1 3 2.4 176 162 0 CGGUUGGAU-==C======U.-\1" "VbrFurni\1" " VbrFurni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1" "VblVulni\1" " VblVulni 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1" "VbhChole\1" " VbhChole 1 3 2.4 176 162 0 GCGCUGGAU-==C======U.-\1" "AclPleur\1" " AclPleur 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1" "PtVVVulg\1" " PtVVVulg 1 3 2.5 176 162 0 CGGUUGGAU-==C======A.-\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); } { const char *arguments[] = { "prgnamefake", "matchsequence=GAGCGGUCAG", // similar to a region where dots occur in seqdata NULp, // matchmismatches "matchacceptN=0", "matchlimitN=4", }; CCP expectd0 = ""; CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1" "BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1"; CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1" "BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1" "Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1"; // this probe-match is also tested with 'arb_probe_match'. see arb_test.cxx@TEST_arb_probe_match CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAG'\1" "BcSSSS00\1" " BcSSSS00 1 0 1.1 25 21 0 GAUCAAGUC-======A===-AUGGGAGCU\1" "Bl0LLL00\1" " Bl0LLL00 2 0 2.2 25 21 0 GAUCAAGUC-======A=C=-ACGGGAGCU\1" "VbrFurni\1" " VbrFurni 3 0 2.4 68 60 0 GGAUUUGUU-=g====CG==-CGGCGGACG\1" "FrhhPhil\1" " FrhhPhil 3 0 2.8 82 70 0 ACGAGUGGC-=gA===C===-UUGGAAACG\1" "ClfPerfr\1" " ClfPerfr 3 0 3.2 86 74 0 CGGCGGGAC-=g==CU====-AACCUGCGG\1" "HllHalod\1" " HllHalod 3 0 3.6 25 21 0 GAUCAAGUC-======Aa=C-GAUGGAAGC\1" "DlcTolu2\1" " DlcTolu2 3 0 3.6 95 83 0 GGACUGCCC-==Aa==A===-CUAAUACCG\1" "FrhhPhil\1" " FrhhPhil 3 0 4.0 25 21 0 GAUCAAGUC-==A====a=C-AGGUCUUCG\1" "AclPleur\1" " AclPleur 3 0 4.0 29 24 0 GAUCAAGUC-==A====a=C-GGGAAGGGA\1" "ClnCorin\1" " ClnCorin 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1" "CltBotul\1" " CltBotul 3 0 4.1 25 21 0 .AUCAAGUC-=====A=G=A-GCUUCUUCG\1" "CPPParap\1" " CPPParap 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUCCUUCG\1" "ClfPerfr\1" " ClfPerfr 3 0 4.1 25 21 0 GAUCAAGUC-=====A=G=A-GUUUCCUUC\1" "DlcTolu2\1" " DlcTolu2 3 0 4.1 157 143 0 GUAGCCGUU-===GAA====-CGGCUGGAU\1" "PslFlave\1" " PslFlave 3 3 2.4 25 21 0 GAUCAAGUC-=======...-\1" "PtVVVulg\1" " PtVVVulg 3 3 2.4 29 24 0 GAUCAAGUC-=======...-\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3); } { const char *arguments[] = { "prgnamefake", "matchsequence=GAGCGGUCAGGAG", // as above, but continues behind '...' NULp, // matchmismatches "matchweighted=1", // use weighted mismatches }; CCP expectd2 = ""; CCP expectd3 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1" "ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1" "CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1" "CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1" "BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1"; CCP expectd4 = " name---- fullname mis N_mis wmis pos ecoli rev 'GAGCGGUCAGGAG'\1" "ClnCorin\1" " ClnCorin 6 0 3.4 77 66 0 AUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1" "CltBotul\1" " CltBotul 6 0 3.4 77 66 0 GUGGAUUAG-Cg====A=g==CC-UUUCGAAAG\1" "CPPParap\1" " CPPParap 6 0 3.4 77 66 0 ACGGAUUAG-Cg====A=g==CC-UUCCGAAAG\1" "BcSSSS00\1" " BcSSSS00 3 0 3.4 25 21 0 GAUCAAGUC-======A===AU=-GGAGCUUGC\1" "ClfPerfr\1" " ClfPerfr 6 0 3.9 121 108 0 AUCAUAAUG-C====A=ug==gU-GAAGUCGUA\1" "ClnCorin\1" " ClnCorin 6 0 3.9 122 109 0 CGCAUAAGA-C====A=ug==gU-GAAGUCGUA\1" "CltBotul\1" " CltBotul 6 0 3.9 122 109 0 CUCAUAAGA-C====A=ug==gU-GAAGUCGUA\1" "CPPParap\1" " CPPParap 6 0 3.9 122 109 0 GCAUAAGAU-C====A=ug==gU-AAGUCGUAA\1" "DcdNodos\1" " DcdNodos 6 0 4.2 77 66 0 GUAACCUAG-Ug====A=g=AC=-UAUGGAAAC\1" "PsAAAA00\1" " PsAAAA00 6 0 4.2 77 66 0 UGGAUUCAG-Cg====A=g=AC=-UCCGGAAAC\1" "PslFlave\1" " PslFlave 6 0 4.2 77 66 0 CUGAUUCAG-Cg====A=g=AC=-UUUCGAAAG\1" "FrhhPhil\1" " FrhhPhil 5 0 4.2 149 135 0 UAACAAUGG-U===C==ag===A-CCUGCGGCU\1" "AclPleur\1" " AclPleur 4 0 4.3 29 24 0 GAUCAAGUC-==A====a=C=g=-AAGGGAGCU\1" "PbcAcet2\1" " PbcAcet2 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1" "PbrPropi\1" " PbrPropi 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1" "Stsssola\1" " Stsssola 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1" "LgtLytic\1" " LgtLytic 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1" "PslFlave\1" " PslFlave 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1" "HllHalod\1" " HllHalod 6 0 4.3 149 135 0 GUAACAAGG-U===C==ag==gA-ACCUGCGGC\1" "VbrFurni\1" " VbrFurni 5 0 4.4 68 60 0 GGAUUUGUU-=g====CG==Cg=-CGGACGGAC\1" "AclPleur\1" " AclPleur 6 0 4.4 35 30 0 GUCGAACGG-U=A===ga===gA-GCUUGCUUU\1" "PslFlave\1" " PslFlave 6 6 4.4 25 21 0 GAUCAAGUC-=======......-\1" "PtVVVulg\1" " PtVVVulg 6 6 4.4 29 24 0 GAUCAAGUC-=======......-\1" "VbrFurni\1" " VbrFurni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1" "VblVulni\1" " VblVulni 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1" "VbhChole\1" " VbhChole 6 0 4.4 149 135 0 GUAACAAGG-U====C=ag==gA-ACCUGGCGC\1"; arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); arguments[2] = "matchmismatches=3"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd3); arguments[2] = "matchmismatches=4"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd4); } // -------------------------- // truncate results { const char *arguments[] = { "prgnamefake", "matchsequence=CANCNCNNUNC", // contains 5N NULp, // matchmismatches "matchacceptN=5", "matchlimitN=7", "matchmaxresults=5", }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1" "BcSSSS00\1" " BcSSSS00 0 5 4.2 176 162 0 CGGCUGGAU-==C=U=CU=U=-U.\1"; // many hits are truncated here: CCP expectd1 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1" "DlcTolu2\1" " DlcTolu2 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU==N-N.\1" "FrhhPhil\1" " FrhhPhil 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1" "HllHalod\1" " HllHalod 1 6 4.9 176 162 0 CGGCUGGAU-==C=U=CU=..-\1" "CPPParap\1" " CPPParap 1 6 4.9 177 163 0 CGGNUGGAU-==C=U=CU=..-\1" "AclPleur\1" " AclPleur 1 6 5.0 176 162 0 CGGUUGGAU-==C=U=CU=A.-\1"; // many hits are truncated here: CCP expectd2 = " name---- fullname mis N_mis wmis pos ecoli rev 'CANCNCNNUNC'\1" "HllHalod\1" " HllHalod 2 5 5.1 45 40 0 AAACGAUGG-a=G=UuGC=U=-CAGGCGUCG\1" "VblVulni\1" " VblVulni 2 5 5.4 49 44 0 AGCACAGAG-a=A=UuGU=U=-UCGGGUGGC\1" "VbrFurni\1" " VbrFurni 2 5 5.7 40 35 0 CGGCAGCGA-==A=AuUGAA=-CUUCGGGGG\1" "LgtLytic\1" " LgtLytic 2 5 6.2 101 89 0 GGGGAAACU-==AGCuAA=A=-CGCAUAAUC\1" "ClfPerfr\1" " ClfPerfr 2 5 6.5 172 158 0 AGGAAGAUU-a=UaC=CC=C=-UUUCU.\1"; arguments[2] = "matchmismatches=0"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); arguments[2] = "matchmismatches=1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd1); arguments[2] = "matchmismatches=2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd2); } // ------------------------------------------------------------- // tests related to http://bugs.arb-home.de/ticket/410 { const char *arguments[] = { "prgnamefake", "matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACC", // length=29 NULp, // matchmismatches "matchacceptN=5", "matchlimitN=7", "matchmaxresults=10", }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACC'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-=============================-GGAUGGUGA\1" "Bl0LLL00\1" " Bl0LLL00 0 0 0.0 84 72 0 CAGCGGCGG-=============================-GGAUGCUGA\1" "AclPleur\1" " AclPleur 4 0 4.6 84 72 0 GAGUGGCGG-=======a========u=UA=========-GCGUAAUCA\1" "PtVVVulg\1" " PtVVVulg 4 0 5.1 84 72 0 GAGCGGCGG-=======a=U======G=U==========-GCAUGACCA\1" "DsssDesu\1" " DsssDesu 5 0 5.3 84 72 0 GAGUGGCGC-========u=C====Gu==A=========-GGAUACAGA\1" "PsAAAA00\1" " PsAAAA00 5 0 5.3 84 72 0 CAGCGGCGG-======gu=C======G==C=========-GCAUACGCA\1"; arguments[2] = "matchmismatches=5"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); } { const char *arguments[] = { "prgnamefake", "matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length=38 NULp, // matchmismatches "matchacceptN=5", "matchlimitN=7", "matchmaxresults=100", }; CCP expectd0 = " name---- fullname mis N_mis wmis pos ecoli rev 'ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA'\1" "BcSSSS00\1" " BcSSSS00 0 0 0.0 84 72 0 UAGCGGCGG-======================================-UGAUUGGGG\1" "Bl0LLL00\1" " Bl0LLL00 1 0 1.5 84 72 0 CAGCGGCGG-==================================C===-UGAUUGGGG\1" "DsssDesu\1" " DsssDesu 8 0 9.4 84 72 0 GAGUGGCGC-========u=C====Gu==A=============ACA==-G.\1" "PtVVVulg\1" " PtVVVulg 8 0 10.7 84 72 0 GAGCGGCGG-=======a=U======G=U===========C===ACC=-UGACUGGGG\1" "AclPleur\1" " AclPleur 9 0 10.8 84 72 0 GAGUGGCGG-=======a========u=UA==========Cg=AA=C=-UGACUGGGG\1" "PsAAAA00\1" " PsAAAA00 10 0 11.9 84 72 0 CAGCGGCGG-======gu=C======G==C==========C==ACgC=-UGGUAACAA\1" "LgtLytic\1" " LgtLytic 10 0 12.8 84 72 0 GAGNGGCGA-=======uG=======uCAA==========C==AA=C=-UGACUGGGG\1" "VbrFurni\1" " VbrFurni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1" "VblVulni\1" " VblVulni 10 0 12.8 84 72 0 GAGCGGCGG-======CauU======GAU===========C===A=C=-UGACUGGGG\1" "Stsssola\1" " Stsssola 10 0 12.9 84 72 0 AAGUGGCGC-======gG=U======G=UC=============AACA=-UGAUUGGGG\1" "DlcTolu2\1" " DlcTolu2 10 0 13.4 84 72 0 GAGUGGCGC-=======G=CC====GGACA==============AA==-UAAUUGGGG\1" "PbcAcet2\1" " PbcAcet2 11 0 12.2 84 72 0 AAGUGGCGC-======A=uUC====GG==U=============AAg=g-UAACUGGGG\1" "HllHalod\1" " HllHalod 11 0 13.0 84 72 0 GAGCGGCGG-======CuG=======uCA===========C==ACgC=-UGACUGGGG\1" "PbrPropi\1" " PbrPropi 12 0 13.6 84 72 0 UAGUGGCGC-======A=uUC====Ga==U=========U===AAg=g-UGACUGGGG\1" "DcdNodos\1" " DcdNodos 12 0 14.4 84 72 0 UAGUGGCGG-======guaU======GUAC==========C==AAg==-UGACUGGGG\1" "VbhChole\1" " VbhChole 12 0 15.4 84 72 0 GAGCGGCGG-======CauU======GAU===========C==AACC=-UGACUGGGG\1"; arguments[2] = "matchmismatches=12"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expectd0); } // test expected errors { const char *arguments[] = { "prgnamefake", "matchsequence=ACGGACUCCGGGAAACCGGGGCUAAUACCGGAUGGUGA", // length = 38 "matchmismatches=20", }; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, "Max. 19 mismatches are allowed for probes of length 38"); } } static char *extract_locations(const char *probe_design_result) { const char *Target = strstr(probe_design_result, "\nTarget"); if (Target) { const char *designed = strchr(Target+7, '\n'); if (designed) { ++designed; GBS_strstruct result(300); RegExpr reg_designed("^[A-Z]+" "[[:space:]]+[0-9]+" "[[:space:]]+([A-Z][=+-])" // subexpr #1 (loc+-=) "[[:space:]]*([0-9]+)", // subexpr #2 (abs or locrel) true); while (designed) { const char *eol = strchr(designed, '\n'); const RegMatch *match = reg_designed.match(designed); if (!match) break; match = reg_designed.subexpr_match(1); if (!match) break; std::string loc = match->extract(designed); match = reg_designed.subexpr_match(2); if (!match) break; std::string pos = match->extract(designed); result.cat(loc.c_str()); result.cat(pos.c_str()); designed = eol ? eol+1 : NULp; } arb_assert(implicated(designed, !reg_designed.has_failed())); // assert RegExpr compiled return result.release(); } } return ARB_strdup("can't extract"); } inline const char *next_line(const char *this_line) { const char *lf = strchr(this_line, '\n'); return (lf && lf[1] && strchr("ACGTU", lf[1])) ? lf+1 : NULp; } inline int count_hits(const char *design_result) { const char *target = strstr(design_result, "\nTarget"); if (target) { const char *hit = next_line(target+1); int hits = 0; while (hit) { ++hits; hit = next_line(hit); } return hits; } return -1; } void TEST_SLOW_design_probe() { // test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb bool use_gene_ptserver = false; { int hits_len_18; { const char *arguments[] = { "prgnamefake", "designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr", "designmintargets=100", }; const char *expected = "Probe design parameters:\n" "Length of probe 18\n" "Temperature [ 0.0 -400.0]\n" "GC-content [30.0 - 80.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 0\n" "Min. group hits 100% (max. rejected coverage: 75%)\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "CGAAAGGAAGAUUAAUAC 18 A=94 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG | - - - - - - - - - - - - - - - - - - - -\n" "GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC | - - - - - - - - - - - - - - - - - - - -\n" "UCAAGUCGAGCGAUGAAG 18 B=18 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA | - - - - - - - - - - - - - - - 2 2 2 2 2\n" "AUCAAGUCGAGCGAUGAA 18 B- 1 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU | - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); hits_len_18 = count_hits(expected); TEST_EXPECT_EQUAL(hits_len_18, 4); // test extraction of positions: { char *positions = extract_locations(expected); TEST_EXPECT_EQUAL(positions, "A=94A+1B=18B-1"); free(positions); } } // same as above with probelength 17 int hits_len_17; { const char *arguments[] = { "prgnamefake", "designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr", "designmintargets=100", "designprobelength=17", }; const char *expected = "Probe design parameters:\n" "Length of probe 17\n" "Temperature [ 0.0 -400.0]\n" "GC-content [30.0 - 80.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 0\n" "Min. group hits 100% (max. rejected coverage: 75%)\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "CAAGUCGAGCGAUGAAG 17 A=19 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG | - - - - - - - - - - - - - - - - 2 2 2 2\n" "UCAAGUCGAGCGAUGAA 17 A- 1 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA | - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n" "AUCAAGUCGAGCGAUGA 17 A- 2 16 33 4 47.1 50.0 UCAUCGCUCGACUUGAU | - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2 4\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); hits_len_17 = count_hits(expected); TEST_EXPECT_EQUAL(hits_len_17, 3); } // same as above with probelength 16 int hits_len_16; { const char *arguments[] = { "prgnamefake", "designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr", "designmintargets=100", "designprobelength=16", }; const char *expected = "Probe design parameters:\n" "Length of probe 16\n" "Temperature [ 0.0 -400.0]\n" "GC-content [30.0 - 80.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 0\n" "Min. group hits 100% (max. rejected coverage: 75%)\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG | - - - - - - - - - - - - - - - - - - - -\n" "AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU | - - - - - - - - - - - - - - - - - - - -\n" "AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU | - - - - - - - - - - - - - - - - - 2 2 2\n" "CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG | - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n" "UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA | - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n" "AUCAAGUCGAGCGAUG 16 B- 3 16 21 4 50.0 48.0 CAUCGCUCGACUUGAU | - - - - - 2 2 2 2 2 2 2 2 2 2 2 2 9 9 9\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); hits_len_16 = count_hits(expected); TEST_EXPECT_EQUAL(hits_len_16, 6); } // combine the 3 preceeding designs int combined_hits; { const char *arguments[] = { "prgnamefake", "designnames=ClnCorin#CltBotul#CPPParap#ClfPerfr", "designmintargets=100", "designprobelength=16", "designmaxprobelength=18", }; const char *expected = "Probe design parameters:\n" "Length of probe 16-18\n" "Temperature [ 0.0 -400.0]\n" "GC-content [30.0 - 80.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 0\n" "Min. group hits 100% (max. rejected coverage: 75%)\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "CGAAAGGAAGAUUAAU 16 A=94 82 77 4 31.2 42.0 AUUAAUCUUCCUUUCG | - - - - - - - - - - - - - - - - - - - -\n" "CGAAAGGAAGAUUAAUAC 18 A+ 0 82 77 4 33.3 48.0 GUAUUAAUCUUCCUUUCG | - - - - - - - - - - - - - - - - - - - -\n" "GAAAGGAAGAUUAAUACC 18 A+ 1 83 77 4 33.3 48.0 GGUAUUAAUCUUCCUUUC | - - - - - - - - - - - - - - - - - - - -\n" "AAGGAAGAUUAAUACC 16 A+ 3 85 77 4 31.2 42.0 GGUAUUAAUCUUCCUU | - - - - - - - - - - - - - - - - - - - -\n" "AAGUCGAGCGAUGAAG 16 B=20 19 69 4 50.0 48.0 CUUCAUCGCUCGACUU | - - - - - - - - - - - - - - - - - 2 2 2\n" "CAAGUCGAGCGAUGAAG 17 B- 1 18 65 4 52.9 52.0 CUUCAUCGCUCGACUUG | - - - - - - - - - - - - - - - - 2 2 2 2\n" "UCAAGUCGAGCGAUGAAG 18 B- 2 17 61 4 50.0 54.0 CUUCAUCGCUCGACUUGA | - - - - - - - - - - - - - - - 2 2 2 2 2\n" "UCAAGUCGAGCGAUGAA 17 B- 2 17 49 4 47.1 50.0 UUCAUCGCUCGACUUGA | - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n" "CAAGUCGAGCGAUGAA 16 B- 1 18 49 4 50.0 48.0 UUCAUCGCUCGACUUG | - - - - - - - - - - - - 2 2 2 2 2 2 2 2\n" "AUCAAGUCGAGCGAUGAA 18 B- 3 16 45 4 44.4 52.0 UUCAUCGCUCGACUUGAU | - - - - - - - - - - - 2 2 2 2 2 2 2 2 2\n" "UCAAGUCGAGCGAUGA 16 B- 2 17 37 4 50.0 48.0 UCAUCGCUCGACUUGA | - - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2\n" "AUCAAGUCGAGCGAUGA 17 B- 3 16 33 4 47.1 50.0 UCAUCGCUCGACUUGAU | - - - - - - - - 2 2 2 2 2 2 2 2 2 2 2 4\n" "AUCAAGUCGAGCGAUG 16 B- 3 16 21 4 50.0 48.0 CAUCGCUCGACUUGAU | - - - - - 2 2 2 2 2 2 2 2 2 2 2 2 9 9 9\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); combined_hits = count_hits(expected); } // check that combined design reports all probes reported by single designs: TEST_EXPECT_EQUAL(combined_hits, hits_len_16+hits_len_17+hits_len_18); } // test vs bug (fails with [8988] .. [9175]) { const char *arguments[] = { "prgnamefake", "designnames=VbhChole#VblVulni", "designmintargets=50", // hit at least 1 of the 2 targets "designmingc=60", "designmaxgc=75", // specific GC range }; const char *expected = "Probe design parameters:\n" "Length of probe 18\n" "Temperature [ 0.0 -400.0]\n" "GC-content [60.0 - 75.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 0 (lowest rejected nongroup hits: 1)\n" "Min. group hits 50%\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "AGUCGAGCGGCAGCACAG 18 A=21 20 39 2 66.7 60.0 CUGUGCUGCCGCUCGACU | - - - - - - - - - - - - - - - - - - - -\n" "GUCGAGCGGCAGCACAGA 18 A+ 1 21 39 2 66.7 60.0 UCUGUGCUGCCGCUCGAC | - - - - - - - - - - - - - - - - - - - -\n" "UCGAGCGGCAGCACAGAG 18 A+ 2 21 39 2 66.7 60.0 CUCUGUGCUGCCGCUCGA | - - - - - - - - - - - - - - - - - - - -\n" "AAGUCGAGCGGCAGCACA 18 A- 1 19 25 2 61.1 58.0 UGUGCUGCCGCUCGACUU | - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n" "CGAGCGGCAGCACAGAGA 18 A+ 3 21 20 1 66.7 60.0 UCUCUGUGCUGCCGCUCG | - - - - - - - - - - - - - - - - - - - -\n" "CGAGCGGCAGCACAGAGG 18 A+ 3 21 20 1 72.2 62.0 CCUCUGUGCUGCCGCUCG | - - - - - - - - - - - - - - - - - - - -\n" "GAGCGGCAGCACAGAGAA 18 A+ 4 21 20 1 61.1 58.0 UUCUCUGUGCUGCCGCUC | - - - - - - - - - - - - - - - - - - - -\n" "GAGCGGCAGCACAGAGGA 18 A+ 4 21 20 1 66.7 60.0 UCCUCUGUGCUGCCGCUC | - - - - - - - - - - - - - - - - - - - -\n" "AGCGGCAGCACAGAGGAA 18 A+ 5 21 20 1 61.1 58.0 UUCCUCUGUGCUGCCGCU | - - - - - - - - - - - - - - - - - - - -\n" "GCGGCAGCACAGAGAAAC 18 A+ 6 22 20 1 61.1 58.0 GUUUCUCUGUGCUGCCGC | - - - - - - - - - - - - - - - - - - - -\n" "GCGGCAGCACAGAGGAAC 18 A+ 6 22 20 1 66.7 60.0 GUUCCUCUGUGCUGCCGC | - - - - - - - - - - - - - - - - - - - -\n" "CGGCAGCACAGAGGAACU 18 A+ 7 23 20 1 61.1 58.0 AGUUCCUCUGUGCUGCCG | - - - - - - - - - - - - - - - - - - - -\n" "CUUGUUCCUUGGGUGGCG 18 B=52 47 20 1 61.1 58.0 CGCCACCCAAGGAACAAG | - - - - - - - - - - - - - - - - - - - -\n" "CUUGUUUCUCGGGUGGCG 18 B+ 0 47 20 1 61.1 58.0 CGCCACCCGAGAAACAAG | - - - - - - - - - - - - - - - - - - - -\n" "UGUUCCUUGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCAAGGAACA | - - - - - - - - - - - - - - - - - - - -\n" "UGUUUCUCGGGUGGCGAG 18 B+ 2 49 20 1 61.1 58.0 CUCGCCACCCGAGAAACA | - - - - - - - - - - - - - - - - - - - -\n" "GUUCCUUGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCAAGGAAC | - - - - - - - - - - - - - - - - - - - -\n" "GUUUCUCGGGUGGCGAGC 18 B+ 3 50 20 1 66.7 60.0 GCUCGCCACCCGAGAAAC | - - - - - - - - - - - - - - - - - - - -\n" "UUCCUUGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCAAGGAA | - - - - - - - - - - - - - - - - - - - -\n" "UUUCUCGGGUGGCGAGCG 18 B+10 57 20 1 66.7 60.0 CGCUCGCCACCCGAGAAA | - - - - - - - - - - - - - - - - - - - -\n" "UCCUUGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCAAGGA | - - - - - - - - - - - - - - - - - - - -\n" "UUCUCGGGUGGCGAGCGG 18 B+11 58 20 1 72.2 62.0 CCGCUCGCCACCCGAGAA | - - - - - - - - - - - - - - - - - - - -\n" "CAAGUCGAGCGGCAGCAC 18 A- 2 18 13 2 66.7 60.0 GUGCUGCCGCUCGACUUG | - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "UCAAGUCGAGCGGCAGCA 18 A- 3 17 3 2 61.1 58.0 UGCUGCCGCUCGACUUGA | - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } // design MANY probes to test location specifier { const char *arguments_loc[] = { "prgnamefake", // "designnames=Stsssola#Stsssola", // @@@ crashes the ptserver "designnames=CPPParap#PsAAAA00", "designmintargets=50", // hit at least 1 of the 2 targets "designmingc=0", "designmaxgc=100", // allow all GCs "designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg "designmishit=7", // allow enough outgroup hits "designprobelength=9", }; const char *expected_loc = "A=29B=51B+1C=99A+8D=112E=80E+2E+3E+4B-1A-5B-6B-5F=124F+1B-2E-7B+0C-5E+2E-1D-1E+6E+7E+8G=89C-2A-1H=61A-6C-1C-3E+3B+3B+4B+5E+5C+1E+4E+6E+7E+8C-7C-6E+5H+1H+2E-6C-4I=152I+1A-7"; TEST_ARB_PROBE_FILT(ARRAY_ELEMS(arguments_loc), arguments_loc, extract_locations, expected_loc); } // same as above { const char *arguments[] = { "prgnamefake", "designnames=CPPParap#PsAAAA00", "designmintargets=50", // hit at least 1 of the 2 targets "designmingc=0", "designmaxgc=100", // allow all GCs "designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg "designmishit=7", // allow enough outgroup hits "designprobelength=9", }; const char *expected = "Probe design parameters:\n" "Length of probe 9\n" "Temperature [30.0 -100.0]\n" "GC-content [ 0.0 -100.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 7 (lowest rejected nongroup hits: 9)\n" "Min. group hits 50%\n" "Target le apos ecol qual grps G+C temp Probe | Decrease T by n*.3C -> probe matches n non group species\n" "GAGCGGAUG 9 A= 29 24 20 1 66.7 30.0 CAUCCGCUC | - - - - - - - - - - - - - - - - - - - -\n" "UGCUCCUGG 9 B= 51 46 20 1 66.7 30.0 CCAGGAGCA | - - - - - - - - - - - - - - - - - - - -\n" "GCUCCUGGA 9 B+ 1 47 20 1 66.7 30.0 UCCAGGAGC | - - - - - - - - - - - - - - - - - - - -\n" "CGGGCGCUA 9 C= 99 87 20 1 77.8 32.0 UAGCGCCCG | - - - - - - - - - - - - - - - - - - - -\n" "GAAGGGAGC 9 A+ 8 32 20 1 66.7 30.0 GCUCCCUUC | 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2\n" "CGCAUACGC 9 D=112 100 20 1 66.7 30.0 GCGUAUGCG | 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2\n" "CGGACGGGC 9 E= 80 69 20 1 88.9 34.0 GCCCGUCCG | 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3\n" "GGACGGGCC 9 E+ 2 70 20 1 88.9 34.0 GGCCCGUCC | 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n" "GACGGGCCU 9 E+ 3 71 20 1 77.8 32.0 AGGCCCGUC | 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n" "ACGGGCCUU 9 E+ 4 72 20 1 66.7 30.0 AAGGCCCGU | 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n" "UCCUUCGGG 9 B- 1 45 20 1 66.7 30.0 CCCGAAGGA | 2 2 2 2 2 2 2 2 2 2 2 2 3 4 4 4 4 4 4 4\n" "CGAGCGAUG 9 A- 5 21 20 1 66.7 30.0 CAUCGCUCG | 3 3 3 3 3 3 3 3 3 3 5 5 5 5 5 5 5 5 5 5\n" "GGGAGCUUG 9 B- 6 40 20 1 66.7 30.0 CAAGCUCCC | 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 5 5\n" "GGAGCUUGC 9 B- 5 41 20 1 66.7 30.0 GCAAGCUCC | 4 4 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5\n" "GCGAUUGGG 9 F=124 111 20 1 66.7 30.0 CCCAAUCGC | 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 6 6\n" "CGAUUGGGG 9 F+ 1 112 20 1 66.7 30.0 CCCCAAUCG | 3 3 3 3 3 3 6 6 6 6 6 6 6 6 6 6 6 6 6 6\n" "GCUUGCUCC 9 B- 2 44 20 1 66.7 30.0 GGAGCAAGC | 4 4 4 4 4 4 5 5 5 5 5 5 5 7 7 7 7 8 8 8\n" "UUAGCGGCG 9 E- 7 62 19 1 66.7 30.0 CGCCGCUAA | 4 4 4 4 4 4 4 4 5 5 5 5 5 5 5 6 6 6 11 11\n" "CCUUCGGGA 9 B+ 0 46 18 1 66.7 30.0 UCCCGAAGG | 2 2 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 5 5 13\n" "GGAAACGGG 9 C- 5 82 17 1 66.7 30.0 CCCGUUUCC | - - - - - - - - - - - - - - - - 3 3 3 3\n" "GGACGGACG 9 E+ 2 70 17 1 77.8 32.0 CGUCCGUCC | 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 10 10 14 14\n" "GCGGACGGG 9 E- 1 68 17 1 88.9 34.0 CCCGUCCGC | 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 13 13 13 13\n" "CCGCAUACG 9 D- 1 99 16 1 66.7 30.0 CGUAUGCGG | 2 2 2 2 2 2 2 2 2 2 2 4 4 4 4 5 5 5 5 5\n" "GGACGUCCG 9 E+ 6 74 14 1 77.8 32.0 CGGACGUCC | - - - - - - - - - - - - - 1 1 1 1 3 3 3\n" "GACGUCCGG 9 E+ 7 75 14 1 77.8 32.0 CCGGACGUC | - - - - - - - - - - - - - 1 1 1 1 2 2 14\n" "ACGUCCGGA 9 E+ 8 76 14 1 66.7 30.0 UCCGGACGU | - - - - - - - - - - - - - 1 1 11 11 12 12 17\n" "CGUCCGGAA 9 G= 89 77 14 1 66.7 30.0 UUCCGGACG | - - - - - - - - - - - - - 1 1 1 1 2 2 2\n" "AACGGGCGC 9 C- 2 85 14 1 77.8 32.0 GCGCCCGUU | - - - - - - - - - - - - - 1 1 1 1 1 1 2\n" "CGAGCGGAU 9 A- 1 23 13 1 66.7 30.0 AUCCGCUCG | - - - - - - - - - - - - 3 3 3 3 3 3 3 3\n" "UUCAGCGGC 9 H= 61 56 13 1 66.7 30.0 GCCGCUGAA | 1 1 1 1 1 1 2 2 2 2 2 2 3 4 4 4 4 4 7 7\n" "UCGAGCGGA 9 A- 6 21 13 1 66.7 30.0 UCCGCUCGA | 3 3 3 3 3 3 3 3 3 3 3 3 8 8 8 8 8 8 8 8\n" "ACGGGCGCU 9 C- 1 86 12 1 77.8 32.0 AGCGCCCGU | - - - - - - - - - - - 1 1 1 1 1 1 2 2 2\n" "AAACGGGCG 9 C- 3 84 9 1 66.7 30.0 CGCCCGUUU | - - - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1\n" "GACGGACGU 9 E+ 3 71 9 1 66.7 30.0 ACGUCCGUC | 2 2 2 2 2 2 2 2 13 13 13 13 13 13 13 14 14 14 14 14\n" "UCGGGAACG 9 B+ 3 49 7 1 66.7 30.0 CGUUCCCGA | - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "CGGGAACGG 9 B+ 4 50 7 1 77.8 32.0 CCGUUCCCG | - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "GGGAACGGA 9 B+ 5 51 7 1 66.7 30.0 UCCGUUCCC | - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "CGGACGUCC 9 E+ 5 73 7 1 77.8 32.0 GGACGUCCG | - - - - - - 1 1 1 1 1 1 1 3 3 3 3 12 12 12\n" "GGGCGCUAA 9 C+ 1 88 7 1 66.7 30.0 UUAGCGCCC | - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "ACGGACGUC 9 E+ 4 72 7 1 66.7 30.0 GACGUCCGU | - - - - - - 2 2 3 3 3 4 4 4 4 5 5 5 5 13\n" "GGGCCUUCC 9 E+ 6 74 7 1 77.8 32.0 GGAAGGCCC | - - - - - - 2 2 2 2 2 3 3 3 3 3 3 3 3 4\n" "GGCCUUCCG 9 E+ 7 75 7 1 77.8 32.0 CGGAAGGCC | - - - - - - 2 2 2 2 2 3 3 3 3 3 3 3 3 3\n" "GCCUUCCGA 9 E+ 8 76 7 1 66.7 30.0 UCGGAAGGC | - - - - - - 2 2 2 2 2 3 3 3 3 3 3 3 3 3\n" "CCGGAAACG 9 C- 7 80 7 1 66.7 30.0 CGUUUCCGG | - - - - - - 2 2 2 2 2 2 2 6 7 9 9 10 10 10\n" "CGGAAACGG 9 C- 6 81 7 1 66.7 30.0 CCGUUUCCG | - - - - - - 2 2 4 4 4 4 4 4 5 5 6 6 6 6\n" "CGGGCCUUC 9 E+ 5 73 7 1 77.8 32.0 GAAGGCCCG | 1 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n" "UCAGCGGCG 9 H+ 1 57 7 1 77.8 32.0 CGCCGCUGA | 2 2 2 2 2 2 6 6 6 6 6 6 6 6 6 6 7 7 7 7\n" "CAGCGGCGG 9 H+ 2 58 7 1 88.9 34.0 CCGCCGCUG | 2 2 2 2 2 2 6 6 6 6 6 6 6 7 12 12 12 12 12 12\n" "UAGCGGCGG 9 E- 6 63 7 1 77.8 32.0 CCGCCGCUA | 4 4 4 4 4 4 10 10 10 10 10 10 12 14 14 14 14 14 14 14\n" "GAAACGGGC 9 C- 4 83 5 1 66.7 30.0 GCCCGUUUC | - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "GCCGUAGGA 9 I=152 138 3 1 66.7 30.0 UCCUACGGC | 1 1 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 12 12\n" "CCGUAGGAG 9 I+ 1 139 3 1 66.7 30.0 CUCCUACGG | 1 1 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11\n" "GUCGAGCGA 9 A- 7 21 3 1 66.7 30.0 UCGCUCGAC | 3 3 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 13\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } #if defined(ARB_64) #define RES_64 #else // !defined(ARB_64) // results below differ for some(!) 32 bit arb versions (numeric issues?) // (e.g. u1004 behaves like 64bit version; u1204 doesnt in NDEBUG mode) // #define RES_64 // uncomment for u1004 #if defined(DEBUG) #define RES_64 #endif #endif // same as above (with probelen == 8) { const char *arguments[] = { "prgnamefake", "designnames=CPPParap#PsAAAA00", "designmintargets=50", // hit at least 1 of the 2 targets "designmingc=0", "designmaxgc=100", // allow all GCs "designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg // "designmishit=7", "designmishit=15", // @@@ reports more results than with 7 mishits, but no mishits reported below! "designprobelength=8", }; const char *expected = "Probe design parameters:\n" "Length of probe 8\n" "Temperature [30.0 -100.0]\n" "GC-content [ 0.0 -100.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 15\n" "Min. group hits 50%\n" "Target le apos ecol qual grps G+C temp Probe | Decrease T by n*.3C -> probe matches n non group species\n" "GGCGGACG 8 A=78 67 39 2 87.5 30.0 CGUCCGCC | 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n" "GCGGACGG 8 A+ 1 68 39 2 87.5 30.0 CCGUCCGC | 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n" "AGCGGCGG 8 A- 3 64 39 2 87.5 30.0 CCGCCGCU | 11 11 11 11 11 11 11 14 14 14 14 14 14 14 14 14 14 14 14 14\n" "GCGGCGGA 8 A- 2 65 39 2 87.5 30.0 UCCGCCGC | 10 10 11 11 11 11 11 14 14 14 14 14 14 14 14 14 14 14 14 14\n" "CGGCGGAC 8 A- 1 66 39 2 87.5 30.0 GUCCGCCG | 10 10 10 10 10 10 10 13 13 13 13 13 13 13 14 14 14 14 14 14\n" "CGGACGGG 8 A+ 2 69 20 1 87.5 30.0 CCCGUCCG | 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2\n" "GGACGGGC 8 A+ 4 70 20 1 87.5 30.0 GCCCGUCC | 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n" "GACGGGCC 8 A+ 5 71 20 1 87.5 30.0 GGCCCGUC | 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3\n" #if defined(RES_64) "ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU | - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n" "CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG | - - - - - - - - - - - - 1 1 1 1 1 1 1 1\n" "CAGCGGCG 8 C=63 58 8 1 87.5 30.0 CGCCGCUG | 2 2 2 2 2 2 2 6 6 6 6 6 6 6 8 8 8 8 8 8\n"; #else // !defined(RES_64) "ACGGGCGC 8 B=98 86 13 1 87.5 30.0 GCGCCCGU | - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n" "CGGGCGCU 8 B+ 1 87 13 1 87.5 30.0 AGCGCCCG | - - - - - - - - - - - - 1 1 1 1 1 1 1 2\n" "CAGCGGCG 8 C=63 58 8 1 87.5 30.0 CGCCGCUG | 2 2 2 2 2 2 2 6 6 6 6 6 6 6 8 8 8 8 8 10\n"; #endif TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } // same as above (but restricting ecoli-range) { const char *arguments[] = { "prgnamefake", "designnames=CPPParap#PsAAAA00", "designmintargets=50", // hit at least 1 of the 2 targets "designmingc=0", "designmaxgc=100", // allow all GCs "designmintemp=30", "designmaxtemp=100", // allow all temp above 30 deg "designmishit=15", "designprobelength=8", "designminpos=65", "designmaxpos=69", // restrict ecoli-range }; const char *expected = "Probe design parameters:\n" "Length of probe 8\n" "Temperature [30.0 -100.0]\n" "GC-content [ 0.0 -100.0]\n" "E.Coli position [ 65 - 69]\n" "Max. nongroup hits 15\n" "Min. group hits 50%\n" "Target le apos ecol qual grps G+C temp Probe | Decrease T by n*.3C -> probe matches n non group species\n" "GGCGGACG 8 A=78 67 39 2 87.5 30.0 CGUCCGCC | 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n" "GCGGACGG 8 A+ 1 68 39 2 87.5 30.0 CCGUCCGC | 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13\n" "GCGGCGGA 8 A- 2 65 39 2 87.5 30.0 UCCGCCGC | 10 10 11 11 11 11 11 14 14 14 14 14 14 14 14 14 14 14 14 14\n" "CGGCGGAC 8 A- 1 66 39 2 87.5 30.0 GUCCGCCG | 10 10 10 10 10 10 10 13 13 13 13 13 13 13 14 14 14 14 14 14\n" "CGGACGGG 8 A+ 2 69 20 1 87.5 30.0 CCCGUCCG | 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "designnames=ClnCorin#CPPParap#ClfPerfr", "designprobelength=16", "designmintargets=100", "designmishit=2", }; const char *expected = "Probe design parameters:\n" "Length of probe 16\n" "Temperature [ 0.0 -400.0]\n" "GC-content [30.0 - 80.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 2 (lowest rejected nongroup hits: 6)\n" "Min. group hits 100% (max. rejected coverage: 67%)\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "CGAAAGGAAGAUUAAU 16 A=94 82 58 3 31.2 42.0 AUUAAUCUUCCUUUCG | 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "AAGGAAGAUUAAUACC 16 A+ 3 85 58 3 31.2 42.0 GGUAUUAAUCUUCCUU | 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "AAGUCGAGCGAUGAAG 16 B=20 19 52 3 50.0 48.0 CUUCAUCGCUCGACUU | 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3\n" "CAAGUCGAGCGAUGAA 16 B- 1 18 37 3 50.0 48.0 UUCAUCGCUCGACUUG | 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3\n" "GUCGAGCGAUGAAGUU 16 B+ 2 21 31 3 50.0 48.0 AACUUCAUCGCUCGAC | - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n" "UCAAGUCGAGCGAUGA 16 B- 2 17 28 3 50.0 48.0 UCAUCGCUCGACUUGA | 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3\n" "AGUCGAGCGAUGAAGU 16 B+ 1 20 19 3 50.0 48.0 ACUUCAUCGCUCGACU | - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "AUCAAGUCGAGCGAUG 16 B- 3 16 16 3 50.0 48.0 CAUCGCUCGACUUGAU | 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3 3 10 10 10\n" "GAUCAAGUCGAGCGAU 16 B- 4 15 4 3 50.0 48.0 AUCGCUCGACUUGAUC | - 2 2 2 3 3 3 3 10 10 10 10 10 10 10 10 10 10 10 10\n" "UGAUCAAGUCGAGCGA 16 B- 5 14 4 3 50.0 48.0 UCGCUCGACUUGAUCA | - 9 9 9 9 9 9 9 10 10 10 10 10 10 10 10 10 10 10 10\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } // test same design as above, but add 2 "unknown species" each of which is missing one of the previously designed probes { const char *arguments[] = { "prgnamefake", "designnames=ClnCorin#Unknown1#CPPParap#ClfPerfr#Unknown2", "designprobelength=16", "designmintargets=100", "designmishit=2", // pass sequences for the unknown species "designsequence=---CGAAAGGAAGAUUAAU------------------AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG-GAUCAAGUCGAGCGAU-UGAUCAAGUCGAGCGA", "designsequence=---CGAAAGGAAGAUUAAU-AAGGAAGAUUAAUACC-AAGUCGAGCGAUGAAG-CAAGUCGAGCGAUGAA-GUCGAGCGAUGAAGUU-UCAAGUCGAGCGAUGA-AGUCGAGCGAUGAAGU-AUCAAGUCGAGCGAUG------------------UGAUCAAGUCGAGCGA", }; const char *expected = "Probe design parameters:\n" "Length of probe 16\n" "Temperature [ 0.0 -400.0]\n" "GC-content [30.0 - 80.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 2\n" "Min. group hits 100% (max. rejected coverage: 80%)\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "CGAAAGGAAGAUUAAU 16 A=94 82 96 5 31.2 42.0 AUUAAUCUUCCUUUCG | 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" // AAGGAAGAUUAAUACC is not designed here "AAGUCGAGCGAUGAAG 16 B=20 19 86 5 50.0 48.0 CUUCAUCGCUCGACUU | 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3\n" "CAAGUCGAGCGAUGAA 16 B- 1 18 61 5 50.0 48.0 UUCAUCGCUCGACUUG | 1 1 1 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3\n" "GUCGAGCGAUGAAGUU 16 B+ 2 21 51 5 50.0 48.0 AACUUCAUCGCUCGAC | - - - - - - - - - - 1 1 1 1 1 1 1 1 1 1\n" "UCAAGUCGAGCGAUGA 16 B- 2 17 46 5 50.0 48.0 UCAUCGCUCGACUUGA | 1 1 1 1 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3\n" "AGUCGAGCGAUGAAGU 16 B+ 1 20 31 5 50.0 48.0 ACUUCAUCGCUCGACU | - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1 1\n" "AUCAAGUCGAGCGAUG 16 B- 3 16 26 5 50.0 48.0 CAUCGCUCGACUUGAU | 1 1 1 1 1 3 3 3 3 3 3 3 3 3 3 3 3 10 10 10\n" // GAUCAAGUCGAGCGAU is not designed here "UGAUCAAGUCGAGCGA 16 B- 5 14 6 5 50.0 48.0 UCGCUCGACUUGAUCA | - 9 9 9 9 9 9 9 10 10 10 10 10 10 10 10 10 10 10 10\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "designnames=VbrFurni", "designprobelength=8", "designmingc=80", "designmaxgc=100", }; const char *expected = "Probe design parameters:\n" "Length of probe 8\n" "Temperature [ 0.0 -400.0]\n" "GC-content [80.0 -100.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 0 (lowest rejected nongroup hits: 2)\n" "Min. group hits 50%\n" "Target le apos ecol qual grps G+C temp Probe | Decrease T by n*.3C -> probe matches n non group species\n" #if defined(RES_64) "CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG | - - - - - - - - - - - - - - - - - - - -\n" #else // !defined(RES_64) "CGGCAGCG 8 A=28 23 20 1 87.5 30.0 CGCUGCCG | - - - - - - - - - - - - - - - - - - - 3\n" #endif "UGGGCGGC 8 B=67 60 8 1 87.5 30.0 GCCGCCCA | - - - - - - - 1 1 1 1 1 1 1 1 1 1 1 1 1\n" #if defined(RES_64) "CGGCGAGC 8 B+ 4 60 8 1 87.5 30.0 GCUCGCCG | - - - - - - - 2 2 2 2 2 2 2 3 3 3 3 3 3\n" #else // !defined(RES_64) "CGGCGAGC 8 B+ 4 60 8 1 87.5 30.0 GCUCGCCG | - - - - - - - 2 2 2 2 2 2 2 4 4 4 4 4 5\n" #endif "GGGCGGCG 8 B+ 1 60 8 1 100.0 32.0 CGCCGCCC | - - - - - - - 3 3 3 3 3 3 3 3 3 3 3 3 3\n" "GGCGGCGA 8 B+ 2 60 8 1 87.5 30.0 UCGCCGCC | - - - - - - - 3 3 3 3 3 3 3 3 3 3 3 3 3\n" "GCGGCGAG 8 B+ 3 60 3 1 87.5 30.0 CUCGCCGC | - - 1 1 1 1 1 4 4 4 4 4 4 4 4 4 4 4 4 4\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg", "designprobelength=14", "designmintargets=100", "designmishit=4", "designmingc=70", "designmaxgc=100", }; const char *expected = "Probe design parameters:\n" "Length of probe 14\n" "Temperature [ 0.0 -400.0]\n" "GC-content [70.0 -100.0]\n" "E.Coli position [any]\n" "Max. nongroup hits 4\n" "Min. group hits 100% (max. rejected coverage: 80%)\n" "Target le apos ecol qual grps G+C temp Probe sequence | Decrease T by n*.3C -> probe matches n non group species\n" "GAGCGGCGGACGGA 14 A=75 64 21 5 78.6 50.0 UCCGUCCGCCGCUC | - - - - 1 1 1 1 1 1 5 5 9 9 10 10 10 10 10 10\n" "CGAGCGGCGGACGG 14 A- 1 63 21 5 85.7 52.0 CCGUCCGCCGCUCG | - - - - 2 2 2 2 2 2 2 2 2 2 2 2 2 2 9 9\n" "AGCGGCGGACGGAC 14 A+ 0 64 21 5 78.6 50.0 GUCCGUCCGCCGCU | 4 7 7 7 9 9 9 9 9 9 9 9 9 9 9 9 9 10 10 10\n"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "designnames=HllHalod#VbhChole#VblVulni#VbrFurni#PtVVVulg", "designprobelength=14", "designmintargets=100", "designmishit=0", "designmingc=51", "designmaxgc=60", }; const char *expected = ""; // no probes found! TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } } void TEST_SLOW_probe_design_errors() { // test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb bool use_gene_ptserver = false; { const char *arguments[] = { "prgnamefake", "designnames=CPPParap#PsAAAA00", "designprobelength=3", }; const char *expected_error = "Specified min. probe length 3 is below the min. allowed probe length of 8"; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } { const char *arguments[] = { "prgnamefake", "designnames=CPPParap#PsAAAA00", "designprobelength=15", "designmaxprobelength=12", }; const char *expected_error = "Max. probe length 12 is below the specified min. probe length of 15"; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } { const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences"; { const char *arguments[] = { "prgnamefake", "designsequence=", // pass an empty sequence "designprobelength=16", }; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } { const char *arguments[] = { "prgnamefake", "designsequence=-------------", // pass a gap-only sequence "designprobelength=16", }; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } } { const char *arguments[] = { "prgnamefake", "designsequence=ACGTACGTACGTACGT", // pass a long enough (unexpected) sequence "designprobelength=16", }; const char *expected_error = "Got 0 unknown marked species, but 1 custom sequence was added (has to match)"; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } { const char *arguments[] = { "prgnamefake", "designnames=Unknown", // one unknown species "designprobelength=16", }; const char *expected_error = "No species marked - no probes designed"; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } { const char *arguments[] = { "prgnamefake", "designnames=Unknown#CPPParap", // one unknown species, one known species "designprobelength=16", }; const char *expected_error = "Got 1 unknown marked species, but 0 custom sequences were added (has to match)"; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } { const char *expected_error = "Sequence contains only 0 bp. Impossible design request for one of the added sequences"; { const char *arguments[] = { "prgnamefake", "designnames=Unknown", // one unknown species "designsequence=", // pass an empty sequence "designprobelength=16", }; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } { const char *arguments[] = { "prgnamefake", "designnames=Unknown", // one unknown species "designsequence=-------------", // pass a gap-only sequence "designprobelength=16", }; TEST_ARB_PROBE__REPORTS_ERROR(ARRAY_ELEMS(arguments), arguments, expected_error); } } } void TEST_SLOW_match_designed_probe() { // test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb bool use_gene_ptserver = false; const char *arguments[] = { "prgnamefake", "matchsequence=UCAAGUCGAGCGAUGAAG", }; CCP expected = " name---- fullname mis N_mis wmis pos ecoli rev 'UCAAGUCGAGCGAUGAAG'\1" "ClnCorin\1" " ClnCorin 0 0 0.0 18 17 0 .GAGUUUGA-==================-UUCCUUCGG\1" "CltBotul\1" " CltBotul 0 0 0.0 18 17 0 ........A-==================-CUUCUUCGG\1" "CPPParap\1" " CPPParap 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUCCUUCGG\1" "ClfPerfr\1" " ClfPerfr 0 0 0.0 18 17 0 AGAGUUUGA-==================-UUUCCUUCG\1"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } void TEST_SLOW_get_existing_probes() { // test here runs versus database ../UNIT_TESTER/run/TEST_pt_src.arb bool use_gene_ptserver = false; { const char *arguments[] = { "prgnamefake", "iterate=20", "iterate_amount=10", }; CCP expected = "AAACCGGGGCTAATACCGGA;AAACGACTGTTAATACCGCA;AAACGATGGAAGCTTGCTTC;AAACGATGGCTAATACCGCA;AAACGGATTAGCGGCGGGAC;" "AAACGGGCGCTAATACCGCA;AAACGGTCGCTAATACCGGA;AAACGGTGGCTAATACCGCA;AAACGTACGCTAATACCGCA;AAACTCAAGCTAATACCGCA"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "iterate=15", "iterate_amount=20", "iterate_separator=:", }; CCP expected = "AAACCGGGGCTAATA:AAACGACTGTTAATA:AAACGATGGAAGCTT:AAACGATGGCTAATA:AAACGGATTAGCGGC:AAACGGGCGCTAATA:AAACGGTCGCTAATA:" "AAACGGTGGCTAATA:AAACGTACGCTAATA:AAACTCAAGCTAATA:AAACTCAGGCTAATA:AAACTGGAGAGTTTG:AAACTGTAGCTAATA:AAACTTGTTTCTCGG:" "AAAGAGGTGCTAATA:AAAGCTTGCTTTCTT:AAAGGAACGCTAATA:AAAGGAAGATTAATA:AAAGGACAGCTAATA:AAAGGGACTTCGGTC"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "iterate=10", "iterate_amount=5", "iterate_readable=0", }; CCP expected = "\2\2\2\3\3\4\4\4\4\3;\2\2\2\3\4\2\3\5\4\5;\2\2\2\3\4\2\5\4\4\2;\2\2\2\3\4\2\5\4\4\3;\2\2\2\3\4\4\2\5\5\2"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "iterate=3", "iterate_amount=70", "iterate_tu=U", }; CCP expected = "AAA;AAC;AAG;AAU;ACA;ACC;ACG;ACU;AGA;AGC;AGG;AGU;AUA;AUC;AUG;AUU;" "CAA;CAC;CAG;CAU;CCA;CCC;CCG;CCU;CGA;CGC;CGG;CGU;CUA;CUC;CUG;CUU;" "GAA;GAC;GAG;GAU;GCA;GCC;GCG;GCU;GGA;GGC;GGG;GGU;GUA;GUC;GUG;GUU;" "UAA;UAC;UAG;UAU;UCA;UCC;UCG;UCU;UGA;UGC;UGG;UGU;UUA;UUC;UUG;UUU"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } { const char *arguments[] = { "prgnamefake", "iterate=2", "iterate_amount=20", }; CCP expected = "AA;AC;AG;AT;" "CA;CC;CG;CT;" "GA;GC;GG;GT;" "TA;TC;TG;TT"; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, expected); } } // #define TEST_AUTO_UPDATE // uncomment to auto-update expected index dumps void TEST_SLOW_index_dump() { for (int use_gene_ptserver = 0; use_gene_ptserver <= 1; use_gene_ptserver++) { const char *dumpfile = use_gene_ptserver ? "index_gpt.dump" : "index_pt.dump"; char *dumpfile_exp = GBS_global_string_copy("%s.expected", dumpfile); const char *arguments[] = { "prgnamefake", GBS_global_string_copy("dump=%s", dumpfile), }; TEST_ARB_PROBE(ARRAY_ELEMS(arguments), arguments, "ok"); #if defined(TEST_AUTO_UPDATE) TEST_COPY_FILE(dumpfile, dumpfile_exp); #else // !defined(TEST_AUTO_UPDATE) TEST_EXPECT_TEXTFILES_EQUAL(dumpfile_exp, dumpfile); #endif TEST_EXPECT_ZERO_OR_SHOW_ERRNO(unlink(dumpfile)); free((char*)arguments[1]); free(dumpfile_exp); } } #undef TEST_AUTO_UPDATE // -------------------------------------------------------------------------------- #include #include #include using namespace std; typedef set Matches; inline void parseMatches(char*& answer, Matches& matches) { ConstStrArray match_results; GBT_splitNdestroy_string(match_results, answer, "\1", SPLIT_KEEPEMPTY); for (size_t i = 1; i0); bool fewerHitsSeen = false; for (size_t subLen = fullLen-1; !fewerHitsSeen && subLen >= 10; --subLen) { // for each partial sub-probe of 20mer char subProbe[20]; subProbe[subLen] = 0; for (size_t pos = 0; pos+subLen <= fullLen; ++pos) { Matches subHits, onlyFull; memcpy(subProbe, fullProbe+pos, subLen); getMatches(subProbe, subHits); extract_first_but_not_second(fullHits, subHits, onlyFull); if (!onlyFull.empty()) { fprintf(stderr, "TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(\"%s\", \"%s\");\n", subProbe, fullProbe); fewerHitsSeen = true; // only list first wrong hit for each fullProbe } } } } } #endif // -------------------------------------------------------------------------------- static arb_test::match_expectation partial_covers_full_probe(const char *part, const char *full) { using namespace arb_test; using namespace std; expectation_group expected; expected.add(that(strstr(full, part)).does_differ_from_NULL()); expected.add(that(strlen(part)).is_less_than(strlen(full))); { Matches matchFull, matchPart; getMatches(full, matchFull); getMatches(part, matchPart); expected.add(that(matchFull.empty()).is_equal_to(false)); Matches onlyFirst; extract_first_but_not_second(matchFull, matchPart, onlyFirst); string only_hit_by_full = matches2hitlist(onlyFirst); expected.add(that(only_hit_by_full).is_equal_to("")); } return all().ofgroup(expected); } #define TEST_PARTIAL_COVERS_FULL_PROBE(part,full) TEST_EXPECTATION(partial_covers_full_probe(part, full)) #define TEST_PARTIAL_COVERS_FULL_PROBE__BROKEN(part,full) TEST_EXPECTATION__BROKEN(partial_covers_full_probe(part, full)) void TEST_SLOW_unmatched_probes() { TEST_PARTIAL_COVERS_FULL_PROBE("CCUCCUUUCU", "GAUUAAUACCCCUCCUUUCU"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUC", "GGGGAACCUGCGGUUGGAUC"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCA", "GGGAACCUGCGGUUGGAUCA"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCAC", "GGAACCUGCGGUUGGAUCAC"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACC", "GAACCUGCGGUUGGAUCACC"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCU", "AACCUGCGGUUGGAUCACCU"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUC", "ACCUGCGGUUGGAUCACCUC"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCC", "CCUGCGGUUGGAUCACCUCC"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCU", "CUGCGGUUGGAUCACCUCCU"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUU", "UGCGGUUGGAUCACCUCCUU"); TEST_PARTIAL_COVERS_FULL_PROBE("CGGUUGGAUCACCUCCUUA", "GCGGUUGGAUCACCUCCUUA"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUC", "GGGGAACCUGGCGCUGGAUC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCA", "GGGAACCUGGCGCUGGAUCA"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCAC", "GGAACCUGGCGCUGGAUCAC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACC", "GAACCUGGCGCUGGAUCACC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCU", "AACCUGGCGCUGGAUCACCU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUC", "ACCUGGCGCUGGAUCACCUC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCC", "CCUGGCGCUGGAUCACCUCC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCU", "CUGGCGCUGGAUCACCUCCU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUU", "UGGCGCUGGAUCACCUCCUU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCGCUGGAUCACCUCCUUU", "GGCGCUGGAUCACCUCCUUU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCAC", "GGAACCUGCGGCUGGAUCAC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACC", "GAACCUGCGGCUGGAUCACC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCU", "AACCUGCGGCUGGAUCACCU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUC", "ACCUGCGGCUGGAUCACCUC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCC", "CCUGCGGCUGGAUCACCUCC"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCU", "CUGCGGCUGGAUCACCUCCU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUU", "UGCGGCUGGAUCACCUCCUU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUU", "GCGGCUGGAUCACCUCCUUU"); TEST_PARTIAL_COVERS_FULL_PROBE("GCUGGAUCACCUCCUUUC", "CGGCUGGAUCACCUCCUUUC"); // the data of the following tests is located right in front of the dots inserted in [8962] TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAG", "AAUUGAAGAGUUUGAUCAAG"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGU", "AUUGAAGAGUUUGAUCAAGU"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUC", "UUGAAGAGUUUGAUCAAGUC"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCG", "UGAAGAGUUUGAUCAAGUCG"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGA", "GAAGAGUUUGAUCAAGUCGA"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAG", "AAGAGUUUGAUCAAGUCGAG"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGC", "AGAGUUUGAUCAAGUCGAGC"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCG", "GAGUUUGAUCAAGUCGAGCG"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGG", "AGUUUGAUCAAGUCGAGCGG"); TEST_PARTIAL_COVERS_FULL_PROBE("UUUGAUCAAGUCGAGCGGU", "GUUUGAUCAAGUCGAGCGGU"); } void TEST_SLOW_variable_defaults_in_server() { test_setup(false); const char *server_tag = GBS_ptserver_tag(TEST_SERVER_ID); TEST_EXPECT_NO_ERROR(arb_look_and_start_server(AISC_MAGIC_NUMBER, server_tag)); const char *servername = GBS_read_arb_tcp(server_tag); { char *socketname = GBS_global_string_copy(":%s", GB_path_in_ARBHOME("UNIT_TESTER/sok/pt.socket")); TEST_EXPECT_EQUAL(servername, socketname); // as defined in ../lib/arb_tcp_org.dat@ARB_TEST_PT_SERVER free(socketname); } T_PT_MAIN com; T_PT_LOCS locs; GB_ERROR error = NULp; aisc_com *link = aisc_open(servername, com, AISC_MAGIC_NUMBER, &error); TEST_EXPECT_NO_ERROR(error); TEST_REJECT_NULL(link); TEST_EXPECT_ZERO(aisc_create(link, PT_MAIN, com, MAIN_LOCS, PT_LOCS, locs, NULp)); { #define LOCAL(rvar) prev_read_##rvar #define FREE_LOCAL_long(rvar) #define FREE_LOCAL_charp(rvar) free(LOCAL(rvar)) #define FREE_LOCAL(type,rvar) FREE_LOCAL_##type(rvar) #define TEST__READ(type,rvar,expected) \ do { \ TEST_EXPECT_ZERO(aisc_get(link, PT_LOCS, locs, rvar, &(LOCAL(rvar)), NULp)); \ TEST_EXPECT_EQUAL(LOCAL(rvar), expected); \ FREE_LOCAL(type,rvar); \ } while(0) #define TEST_WRITE(type,rvar,val) \ TEST_EXPECT_ZERO(aisc_put(link, PT_LOCS, locs, rvar, (type)val, NULp)) #define TEST_CHANGE(type,rvar,val) \ do { \ TEST_WRITE(type, rvar, val); \ TEST__READ(type, rvar, val); \ } while(0) #define TEST_DEFAULT_CHANGE(ctype,type,remote_variable,default_value,other_value) \ do { \ ctype DEFAULT_VALUE = default_value; \ ctype OTHER_VALUE = other_value; \ type LOCAL(remote_variable); \ TEST__READ(type, remote_variable, DEFAULT_VALUE); \ TEST_CHANGE(type, remote_variable, OTHER_VALUE); \ TEST_CHANGE(type, remote_variable, DEFAULT_VALUE); \ } while(0) TEST_DEFAULT_CHANGE(const long, long, LOCS_MATCH_ALSO_REVCOMP, 1, 67); typedef char *charp; typedef const char *ccharp; TEST_DEFAULT_CHANGE(ccharp, charp, LOCS_LOGINTIME, "notime", "sometime"); } TEST_EXPECT_ZERO(aisc_close(link, com)); link = NULp; } #endif // UNIT_TESTS