def testExtendedAlignment(self): subset = [ "SFIF", "SFII", "SCFC", "SGHD", "SDCC", "SBGE", "SFBB", "SDI", "SCGB", "SJGF", "SGBI", "SCJA", "SGAD", "SHEB", "SFHB", "SDJI", "SHED", "SJJJ", "SBBE", "SCCH", "SDJB", "SDAC", "SHEH", "SFDC", "SFEI", "SHHB", "SC", "SIAB", "SDDI", "SBCB", "SJB", "SEBD", "SFGD", "SHA", "SIDA", "SGHI", "SGIB", "SBFJ", "SFIE", "SCJF", "SJHJ", "SJBG", "SEJI", "SFFF", "SJ", "SIII", "SJHH", "SEIH", "SBDC", "SHDJ", "SJDD", "SGDB", "SIHA", "SIBB", "SECC", "SCAD", "SGBB", "SGIF", "SJHC", "SFCD", "SEAA", "SEFF", "SDFG", "SDJE", "SCFG", "SFH", "SCJ", "SDDD", "SEGD", "SCIH", "SDAG", "SCJE", "SFAJ", "SIDJ", "SE", "SHBC", "SJFF", "SCHD", "SBHA", "SEDF", "SFAF", "SEDD", "SDHD", "SGJD", "SIBH", "SGDF", "SIFA", "SJGA", "SIJB", "SFI", "SGA", "SBFC", "SBJA", "SFFC", "SFDH", "SFEE", "SBDF", "SGBJ", "SDHE", "SJIB", "SHHI", "SIDE", "SJII" ] alg = MutableAlignment() alg.read_filepath(get_data_path("simulated/test.fasta")) alg.delete_all_gap() tlen = alg.get_length() frg = MutableAlignment() frg.read_filepath(get_data_path("simulated/test.fas")) # print frg.get_num_taxa() pp = SeppProblem(list(alg.keys())) pp.fragments = frg pp.subalignment = alg cp1 = SeppProblem(subset, pp) cp2 = SeppProblem(list(set(alg.keys()) - set(subset)), pp) cp1.fragments = ReadonlySubalignment( [k for k in list(frg.keys()) if int(k[-1]) >= 9], frg) cp2.fragments = ReadonlySubalignment( [k for k in list(frg.keys()) if int(k[-1]) <= 1], frg) cp1labels = cp1.write_subalignment_without_allgap_columns( self.fp_dummy1) # tmp/cp1.fasta cp2labels = cp2.write_subalignment_without_allgap_columns( self.fp_dummy2) # tmp/cp2.fasta tmp = MutableAlignment().read_filepath(self.fp_dummy1) assert all( [not tmp.is_all_gap(pos) for pos in range(0, tmp.get_length())]) tmp = MutableAlignment().read_filepath(self.fp_dummy2) assert all( [not tmp.is_all_gap(pos) for pos in range(0, tmp.get_length())]) cp1.fragments.write_to_path(self.fp_dummy3) # tmp/cp1.frags.fas cp2.fragments.write_to_path(self.fp_dummy4) # tmp/cp2.frags.fas '''We have done the hmmalign before. don't worry about that right now''' ext1 = ExtendedAlignment(cp1.fragments) ext1.build_extended_alignment(self.fp_dummy1, get_data_path("tmp/cp1.extended.sto")) ext1.relabel_original_columns(cp1labels) ext2 = ExtendedAlignment(cp2.fragments) ext2.build_extended_alignment(self.fp_dummy2, get_data_path("tmp/cp2.extended.sto")) ext2.relabel_original_columns(cp2labels) extmerger = ExtendedAlignment([]) extmerger.merge_in(ext1) mixed = extmerger.merge_in(ext2) extmerger.write_to_path(self.fp_dummy5) # tmp/extended.merged.fasta assert extmerger.is_aligned(), "Merged alignment is not aligned" in1 = len([x for x in ext1._col_labels if x < 0]) in2 = len([x for x in ext2._col_labels if x < 0]) assert (in1 + in2 + tlen - mixed) == extmerger.get_length(), \ ("Lengths don't match up after merging. Merged:%d. Insertion1:%d " "Insertion2:%d BaseLen:%d Mixed-insertion: %d") % ( extmerger.get_length(), in1, in2, tlen, mixed) assert (in1 + in2 - mixed) == len(extmerger.get_insertion_columns()), \ ("Columns are not correctly labeled after merging. Merged " "insertion count:%d. Insertion1:%d Insertion2:%d Mixed-insertion:" " %d") % ( len(list(extmerger.iter_insertion_columns())), in1, in1, mixed) tmp = extmerger.get_base_readonly_alignment().get_mutable_alignment() tmp.delete_all_gap() assert tmp.is_aligned(), "merged alignment should be aligned!" assert tmp.get_length() == tlen, "merged alignment has wrong length" assert all([alg[k] == s for (k, s) in list(tmp.items())]), \ "merged alignment should match original alignment"
def testExtendedAlignment(self): subset = [ "SFIF", "SFII", "SCFC", "SGHD", "SDCC", "SBGE", "SFBB", "SDI", "SCGB", "SJGF", "SGBI", "SCJA", "SGAD", "SHEB", "SFHB", "SDJI", "SHED", "SJJJ", "SBBE", "SCCH", "SDJB", "SDAC", "SHEH", "SFDC", "SFEI", "SHHB", "SC", "SIAB", "SDDI", "SBCB", "SJB", "SEBD", "SFGD", "SHA", "SIDA", "SGHI", "SGIB", "SBFJ", "SFIE", "SCJF", "SJHJ", "SJBG", "SEJI", "SFFF", "SJ", "SIII", "SJHH", "SEIH", "SBDC", "SHDJ", "SJDD", "SGDB", "SIHA", "SIBB", "SECC", "SCAD", "SGBB", "SGIF", "SJHC", "SFCD", "SEAA", "SEFF", "SDFG", "SDJE", "SCFG", "SFH", "SCJ", "SDDD", "SEGD", "SCIH", "SDAG", "SCJE", "SFAJ", "SIDJ", "SE", "SHBC", "SJFF", "SCHD", "SBHA", "SEDF", "SFAF", "SEDD", "SDHD", "SGJD", "SIBH", "SGDF", "SIFA", "SJGA", "SIJB", "SFI", "SGA", "SBFC", "SBJA", "SFFC", "SFDH", "SFEE", "SBDF", "SGBJ", "SDHE", "SJIB", "SHHI", "SIDE", "SJII"] alg = MutableAlignment() alg.read_filepath(get_data_path("simulated/test.fasta")) alg.delete_all_gap() tlen = alg.get_length() frg = MutableAlignment() frg.read_filepath(get_data_path("simulated/test.fas")) # print frg.get_num_taxa() pp = SeppProblem(list(alg.keys())) pp.fragments = frg pp.subalignment = alg cp1 = SeppProblem(subset, pp) cp2 = SeppProblem(list(set(alg.keys()) - set(subset)), pp) cp1.fragments = ReadonlySubalignment( [k for k in list(frg.keys()) if int(k[-1]) >= 9], frg) cp2.fragments = ReadonlySubalignment( [k for k in list(frg.keys()) if int(k[-1]) <= 1], frg) cp1labels = cp1.write_subalignment_without_allgap_columns( self.fp_dummy1) # tmp/cp1.fasta cp2labels = cp2.write_subalignment_without_allgap_columns( self.fp_dummy2) # tmp/cp2.fasta tmp = MutableAlignment().read_filepath(self.fp_dummy1) assert all([not tmp.is_all_gap(pos) for pos in range(0, tmp.get_length())]) tmp = MutableAlignment().read_filepath(self.fp_dummy2) assert all([not tmp.is_all_gap(pos) for pos in range(0, tmp.get_length())]) cp1.fragments.write_to_path(self.fp_dummy3) # tmp/cp1.frags.fas cp2.fragments.write_to_path(self.fp_dummy4) # tmp/cp2.frags.fas '''We have done the hmmalign before. don't worry about that right now''' ext1 = ExtendedAlignment(cp1.fragments) ext1.build_extended_alignment( self.fp_dummy1, get_data_path("tmp/cp1.extended.sto")) ext1.relabel_original_columns(cp1labels) ext2 = ExtendedAlignment(cp2.fragments) ext2.build_extended_alignment( self.fp_dummy2, get_data_path("tmp/cp2.extended.sto")) ext2.relabel_original_columns(cp2labels) extmerger = ExtendedAlignment([]) extmerger.merge_in(ext1) mixed = extmerger.merge_in(ext2) extmerger.write_to_path(self.fp_dummy5) # tmp/extended.merged.fasta assert extmerger.is_aligned(), "Merged alignment is not aligned" in1 = len([x for x in ext1._col_labels if x < 0]) in2 = len([x for x in ext2._col_labels if x < 0]) assert (in1 + in2 + tlen - mixed) == extmerger.get_length(), \ ("Lengths don't match up after merging. Merged:%d. Insertion1:%d " "Insertion2:%d BaseLen:%d Mixed-insertion: %d") % ( extmerger.get_length(), in1, in2, tlen, mixed) assert (in1 + in2 - mixed) == len(extmerger.get_insertion_columns()), \ ("Columns are not correctly labeled after merging. Merged " "insertion count:%d. Insertion1:%d Insertion2:%d Mixed-insertion:" " %d") % ( len(list(extmerger.iter_insertion_columns())), in1, in1, mixed) tmp = extmerger.get_base_readonly_alignment().get_mutable_alignment() tmp.delete_all_gap() assert tmp.is_aligned(), "merged alignment should be aligned!" assert tmp.get_length() == tlen, "merged alignment has wrong length" assert all([alg[k] == s for (k, s) in list(tmp.items())]), \ "merged alignment should match original alignment"