// ============================================================= // // // // File : pvp.cxx // // Purpose : calculate positional variability (parsimony) // // // // Institute of Microbiology (Technical University Munich) // // http://www.arb-home.de/ // // // // ============================================================= // #include "pvp.h" #include "AP_pos_var.h" #include #include GB_ERROR PVP_calculate(GBDATA *gb_main, const char *ali_name, const char *tree_name, const char *target_SAI_name) { GB_ERROR error = NULp; GB_transaction ta(gb_main); long ali_len = GBT_get_alignment_len(gb_main, ali_name); if (ali_len <= 0) { error = GB_await_error(); } else { const double phase1_fraction = 1.0/650; arb_progress progress(WEIGHTED, "Calculating positional variability", phase1_fraction); progress.subtitle("Loading Tree"); // get tree TreeNode *tree; { tree = GBT_read_tree(gb_main, tree_name, new SimpleRoot); if (!tree) { error = GB_await_error(); } else { GBT_link_tree(tree, gb_main, true, NULp, NULp); } } progress.inc_and_check_user_abort(error); if (!error) { progress.subtitle("Counting mutations"); GB_alignment_type at = GBT_get_alignment_type(gb_main, ali_name); arb_assert(at != GB_AT_UNKNOWN); bool isNUC = at==GB_AT_DNA || at==GB_AT_RNA; AP_pos_var pvp(gb_main, ali_name, ali_len, isNUC, tree_name); error = pvp.delete_aliEntry_from_SAI(target_SAI_name); if (!error) error = pvp.retrieve(tree); if (!error) error = pvp.save_aliEntry_to_SAI(target_SAI_name); progress.inc_and_check_user_abort(error); } destroy(tree); } ta.close(error); return error; } // -------------------------------------------------------------------------------- #ifdef UNIT_TESTS #ifndef TEST_UNIT_H #include #endif static arb_test::match_expectation saidata_equal(GBDATA *gb_main, const char *sainame, const char *aliname, const char *expected_data) { using namespace arb_test; GB_transaction ta(gb_main); GBDATA *gb_sai = GBT_find_SAI(gb_main, sainame); GBDATA *gb_saiali = GB_entry(gb_sai, aliname); GBDATA *gb_saidata = GB_entry(gb_saiali, "data"); const char *saidata = GB_read_char_pntr(gb_saidata); return that(saidata).is_equal_to(expected_data); } static arb_test::match_expectation saitype_equal(GBDATA *gb_main, const char *sainame, const char *aliname, const char *expected_type) { using namespace arb_test; GB_transaction ta(gb_main); GBDATA *gb_sai = GBT_find_SAI(gb_main, sainame); GBDATA *gb_saiali = GB_entry(gb_sai, aliname); GBDATA *gb_saitype = GB_entry(gb_saiali, "_TYPE"); const char *saitype = GB_read_char_pntr(gb_saitype); return that(saitype).is_equal_to(expected_type); } #define TEST_EXPECT_SAIDATA_EQUAL(expected) TEST_EXPECTATION(saidata_equal(gb_main,SAI_name,aliname,expected)) #define TEST_EXPECT_SAITYPE_EQUAL(expected) TEST_EXPECTATION(saitype_equal(gb_main,SAI_name,aliname,expected)) void TEST_pvp() { GB_shell shell; const char *SAI_name = "POS_VAR_BY_PARSIMONY"; { // nuc data: GBDATA *gb_main = GB_open("TEST_nuc.arb", "rw"); const char *aliname = "ali_16s"; TEST_EXPECT_NO_ERROR(PVP_calculate(gb_main, aliname, "tree_nuc", SAI_name)); TEST_EXPECT_SAITYPE_EQUAL("PVP: Positional Variability by Parsimony: tree 'tree_nuc' ntaxa 12"); TEST_EXPECT_SAIDATA_EQUAL(".----222----7------32-7-7----774-----77-----747-77-7-47-----------73--433-.3134--1-41-4-4011222337--" "....-632320124--11141-4-..24312434--3----7-77---7----774-4-4-34--44-77-732777424--7-----3247------44" "33----------2--73063442221633737777326110244-3----73--2--4-773--4-7--3774777137-7774437274-3372--7--" "--7------47-7---24--73--------2-4--7374---74-734------43-777-47-7---3---3----------7-3---3----------" "-----7-----4-7----7--4-4------3--3---3----4-4---4-47-------77---4-----447-7--4-7-----377--7-7434373-" "-77--5412243422747--7-441244321337--777--3434333-77---777---------7------------7-----------7---77--4" "-7----477----4---7-----------4-774-4---7--742237-7-777-7---4---327447----4----43477423-----447-7--77" "21234--7---7477-77777-727777---7-3--4---77------7------7---4--4--4-4---7---7------------47727--47777" "4477-----7--4-7747-------47---7-7-7--------------------------74--7----------43-7--7477-774734-6----7" "47---6-42-447-774-4--------77-----7-34-------7-------747------77-7---------4------------4-----------" "7-----------------------4--4---7-.---7--------74437-------7-3424-732233427--7-72333127-6.--7777---6-" "-424347-------7-------47--------------77----77---------------7------------------77437-77------4-743-" "77-3-77---7----7-3377-------7-7-74--7-7---------7-7---4-------74---7----7------7-3447----7----------" "--------2443----7777-33--2-4444-7--44437---37---7746----34447-47---7----7--4--4----------4--4--7----" "44-----7---------7-4777-----3-77774-7------------7----47---------------------7--7-47---47-774777744-" "--34-7-44227----3...7712.1----123-7742-4-777774-7774----4-3--7--------------------77--447--744--77-7" "---------------3-..."); // tests reported errors: TEST_EXPECT_ERROR_CONTAINS(PVP_calculate(gb_main, "ali_61s", "tree_nuc", SAI_name), "alignment 'ali_61s' not found"); TEST_EXPECT_ERROR_CONTAINS(PVP_calculate(gb_main, "ali_16s", "tree_miss", SAI_name), "tree not found"); GB_close(gb_main); } { // protein data: GBDATA *gb_main = GB_open("TEST_prot.arb", "rw"); const char *aliname = "ali_tuf_pro"; TEST_EXPECT_NO_ERROR(PVP_calculate(gb_main, aliname, "tree_prot", SAI_name)); TEST_EXPECT_SAITYPE_EQUAL("PVP: Positional Variability by Parsimony: tree 'tree_prot' ntaxa 11"); TEST_EXPECT_SAIDATA_EQUAL("-----4-634363-4-3-4666----6--6-6-6666466666664666466666-43-34366633334446-4666-364-6--66666664-44646" "666-4---4-66---6--66-4-66-6666444-6666466666--4--4--6466633346-62--3-3436343243266464433446433434662" "2-4634-663466644346314-23364666646243343-6366-34632-0632-46646-666-43-6-6---46-46-3-3432-32634464334" "443636666-66461612636----64664642421634-3-33444443632334-1-3-64-44664646634-433366666623624426246444" "4436330334446-63434344622344666320664664--666643--66-446341446--6------6--466----------"); GB_close(gb_main); } } #endif // UNIT_TESTS // --------------------------------------------------------------------------------