def testAlignmentReadFasta(self): alg = MutableAlignment() alg.read_filepath(get_data_path("mock/pyrg/sate.fasta")) assert len(alg) == 65, "MutableAlignment length is %s" % len(alg) assert all([not alg.is_all_gap(i) for i in range(0, alg.get_length())])
def testAlignmentReadFasta(self): print "====== starting testAlignmentReadFasta ==========" alg = MutableAlignment() alg.read_filepath("data/mock/pyrg/sate.fasta") print "Maing alignment is:\n\n", alg assert len(alg) == 65, "MutableAlignment length is %s" %len(alg) assert all([not alg.is_all_gap(i) for i in xrange(0,alg.get_length())])
def testAlignmentReadFasta(self): print("====== starting testAlignmentReadFasta ==========") alg = MutableAlignment() alg.read_filepath("data/mock/pyrg/sate.fasta") print("Maing alignment is:\n\n", alg) assert len(alg) == 65, "MutableAlignment length is %s" % len(alg) assert all([not alg.is_all_gap(i) for i in range(0, alg.get_length())])
def testReadOnlySubAlignment(self): print("======= starting testReadOnlySubAlignment =========") alg = MutableAlignment() alg.read_filepath("data/mock/pyrg/sate.fasta") subset = list(alg.keys())[9:12] readonly_subalignment = ReadonlySubalignment(subset, alg) print("subalignment is:\n\n", readonly_subalignment) assert len(readonly_subalignment) == 3, len(readonly_subalignment) assert set(readonly_subalignment.keys()) == set( readonly_subalignment.get_sequence_names()) == set( subset ), "Subalignment keys not matching given keys %s vs %s" % (list( readonly_subalignment.keys()), subset) for (k, s) in list(readonly_subalignment.items()): assert k in subset, "%s not found in subset but returned by subalignment" % k assert s == alg[ k], "sequence associated with %k not matching parent alignment" % k try: readonly_subalignment[2] = "ACGT" assert False, "Readony alignment is successfully modified. " except TypeError: pass assert readonly_subalignment.get_length() == alg.get_length( ), "alignment length should not change" assert readonly_subalignment.is_aligned() == True assert readonly_subalignment.is_all_gap( 2) == True, "Site 2 should be all gaps" assert readonly_subalignment.is_all_gap( 150) == False, "Site 100 should not be all gaps" readonly_subalignment.write_to_path("data/mock/pyrg/sate.sub.fasta") mutable_subalignment = readonly_subalignment.get_mutable_alignment() mutable_subalignment.delete_all_gap() assert all([ not mutable_subalignment.is_all_gap(i) for i in range(0, mutable_subalignment.get_length()) ]) print("======= finishing testReadOnlySubAlignment =========")
def testReadOnlySubAlignment(self): alg = MutableAlignment() alg.read_filepath(get_data_path("mock/pyrg/sate.fasta")) subset = [ 'NC_008701_720717_722309', 'NC_013156_149033_150643', 'NC_013887_802739_801129' ] readonly_subalignment = ReadonlySubalignment(subset, alg) assert len(readonly_subalignment) == 3, len(readonly_subalignment) assert set(readonly_subalignment.keys()) == set( readonly_subalignment.get_sequence_names()) == set(subset), \ "Subalignment keys not matching given keys %s vs %s" % ( list(readonly_subalignment.keys()), subset) for (k, s) in list(readonly_subalignment.items()): assert k in subset, \ "%s not found in subset but returned by subalignment" % k assert s == alg[k], \ "sequence associated with %s not matching parent alignment" % k try: readonly_subalignment[2] = "ACGT" assert False, "Readony alignment is successfully modified. " except TypeError: pass assert readonly_subalignment.get_length() == alg.get_length(), \ "alignment length should not change" assert readonly_subalignment.is_aligned() is True assert readonly_subalignment.is_all_gap(2) is True, \ "Site 2 should be all gaps" assert readonly_subalignment.is_all_gap(150) is False, \ "Site 100 should not be all gaps" readonly_subalignment.write_to_path( self.fp_dummy1) # "mock/pyrg/sate.sub.fasta" mutable_subalignment = readonly_subalignment.get_mutable_alignment() mutable_subalignment.delete_all_gap() assert all([ not mutable_subalignment.is_all_gap(i) for i in range(0, mutable_subalignment.get_length()) ])
def testReadOnlySubAlignment(self): alg = MutableAlignment() alg.read_filepath(get_data_path("mock/pyrg/sate.fasta")) subset = ['NC_008701_720717_722309', 'NC_013156_149033_150643', 'NC_013887_802739_801129'] readonly_subalignment = ReadonlySubalignment(subset, alg) assert len(readonly_subalignment) == 3, len(readonly_subalignment) assert set(readonly_subalignment.keys()) == set( readonly_subalignment.get_sequence_names()) == set(subset), \ "Subalignment keys not matching given keys %s vs %s" % ( list(readonly_subalignment.keys()), subset) for (k, s) in list(readonly_subalignment.items()): assert k in subset, \ "%s not found in subset but returned by subalignment" % k assert s == alg[k], \ "sequence associated with %k not matching parent alignment" % k try: readonly_subalignment[2] = "ACGT" assert False, "Readony alignment is successfully modified. " except TypeError: pass assert readonly_subalignment.get_length() == alg.get_length(), \ "alignment length should not change" assert readonly_subalignment.is_aligned() is True assert readonly_subalignment.is_all_gap(2) is True, \ "Site 2 should be all gaps" assert readonly_subalignment.is_all_gap(150) is False, \ "Site 100 should not be all gaps" readonly_subalignment.write_to_path( self.fp_dummy1) # "mock/pyrg/sate.sub.fasta" mutable_subalignment = readonly_subalignment.get_mutable_alignment() mutable_subalignment.delete_all_gap() assert all([not mutable_subalignment.is_all_gap(i) for i in range(0, mutable_subalignment.get_length())])
def testReadOnlySubAlignment(self): print "======= starting testReadOnlySubAlignment =========" alg = MutableAlignment() alg.read_filepath("data/mock/pyrg/sate.fasta") subset = alg.keys()[9:12] readonly_subalignment = ReadonlySubalignment(subset, alg) print "subalignment is:\n\n", readonly_subalignment assert len(readonly_subalignment) == 3, len(readonly_subalignment) assert readonly_subalignment.keys() == readonly_subalignment.get_sequence_names() == subset, "Subalignment keys not matching given keys %s vs %s" %(readonly_subalignment.keys() , subset) for (k, s) in readonly_subalignment.items(): assert k in subset, "%s not found in subset but returned by subalignment" %k assert s == alg[k], "sequence associated with %k not matching parent alignment" %k try: readonly_subalignment[2] = "ACGT" assert False, "Readony alignment is successfully modified. " except TypeError: pass assert readonly_subalignment.get_length() == alg.get_length(), "alignment length should not change" assert readonly_subalignment.is_aligned() == True assert readonly_subalignment.is_all_gap(2) == True, "Site 2 should be all gaps" assert readonly_subalignment.is_all_gap(150) == False, "Site 100 should not be all gaps" readonly_subalignment.write_to_path("data/mock/pyrg/sate.sub.fasta") mutable_subalignment = readonly_subalignment.get_mutable_alignment() mutable_subalignment.delete_all_gap() assert all([not mutable_subalignment.is_all_gap(i) for i in xrange(0,mutable_subalignment.get_length())]) print "======= finishing testReadOnlySubAlignment ========="
def testExtendedAlignment(self): print "======= starting testExtendedAlignment =========" 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("data/simulated/test.fasta") alg.delete_all_gap() tlen = alg.get_length() frg = MutableAlignment() frg.read_filepath("data/simulated/test.fas") #print frg.get_num_taxa() pp = SeppProblem(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 frg.keys() if int(k[-1]) >= 9], frg) cp2.fragments = ReadonlySubalignment( [k for k in frg.keys() if int(k[-1]) <= 1], frg) cp1labels = cp1.write_subalignment_without_allgap_columns( "data/tmp/cp1.fasta") cp2labels = cp2.write_subalignment_without_allgap_columns( "data/tmp/cp2.fasta") tmp = MutableAlignment().read_filepath("data/tmp/cp1.fasta") assert all( [not tmp.is_all_gap(pos) for pos in xrange(0, tmp.get_length())]) tmp = MutableAlignment().read_filepath("data/tmp/cp2.fasta") assert all( [not tmp.is_all_gap(pos) for pos in xrange(0, tmp.get_length())]) cp1.fragments.write_to_path("data/tmp/cp1.frags.fas") cp2.fragments.write_to_path("data/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("data/tmp/cp1.fasta", "data/tmp/cp1.extended.sto") ext1.relabel_original_columns(cp1labels) ext2 = ExtendedAlignment(cp2.fragments) ext2.build_extended_alignment("data/tmp/cp2.fasta", "data/tmp/cp2.extended.sto") ext2.relabel_original_columns(cp2labels) extmerger = ExtendedAlignment([]) extmerger.merge_in(ext1) mixed = extmerger.merge_in(ext2) extmerger.write_to_path("data/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]) print "Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d" % ( extmerger.get_length(), in1, in2, tlen) 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( list(extmerger.iter_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 tmp.items() ]), "merged alignment should match original alignment" print "======= finished testExtendedAlignment ========="
def testExtendedAlignment(self): print "======= starting testExtendedAlignment =========" 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("data/simulated/test.fasta") alg.delete_all_gap() tlen = alg.get_length() frg = MutableAlignment() frg.read_filepath("data/simulated/test.fas") #print frg.get_num_taxa() pp = SeppProblem(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 frg.keys() if int(k[-1]) >= 9], frg) cp2.fragments = ReadonlySubalignment([k for k in frg.keys() if int(k[-1]) <= 1], frg) cp1labels = cp1.write_subalignment_without_allgap_columns("data/tmp/cp1.fasta") cp2labels = cp2.write_subalignment_without_allgap_columns("data/tmp/cp2.fasta") tmp = MutableAlignment().read_filepath("data/tmp/cp1.fasta") assert all([not tmp.is_all_gap(pos) for pos in xrange(0,tmp.get_length())]) tmp = MutableAlignment().read_filepath("data/tmp/cp2.fasta") assert all([not tmp.is_all_gap(pos) for pos in xrange(0,tmp.get_length())]) cp1.fragments.write_to_path("data/tmp/cp1.frags.fas") cp2.fragments.write_to_path("data/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("data/tmp/cp1.fasta", "data/tmp/cp1.extended.sto") ext1.relabel_original_columns(cp1labels) ext2 = ExtendedAlignment(cp2.fragments) ext2.build_extended_alignment("data/tmp/cp2.fasta", "data/tmp/cp2.extended.sto") ext2.relabel_original_columns(cp2labels) extmerger = ExtendedAlignment([]) extmerger.merge_in(ext1) mixed = extmerger.merge_in(ext2) extmerger.write_to_path("data/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]) print "Merged:%d. Insertion1:%d Insertion2:%d BaseLen:%d" %(extmerger.get_length(),in1 , in2 , tlen) 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(list(extmerger.iter_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 tmp.items()]), "merged alignment should match original alignment" print "======= finished testExtendedAlignment ========="
done = base_alignment.read_filepath(base_alignment_file) # [0] subbackbone = original_backbone.get_soft_sub_alignment( base_alignment.get_sequence_names()) print("Orig alignment sequences: ", original_backbone.get_sequence_names()) print("Base alignment sequences: ", base_alignment.get_sequence_names()) print("num base alignment seqs: ", len(base_alignment.get_sequence_names())) frags = MutableAlignment() sequence_names = [] for file in sequence_files: seq = MutableAlignment() done = seq.read_filepath(file) print('query sequence names:', seq.get_sequence_names()) print("query sequence length:", seq.get_length()) done = sequence_names.extend(seq.get_sequence_names()) for name, seq in seq.items(): frags[name] = seq.upper() problem = SeppProblem(sequence_names) problem.set_subalignment(subbackbone) # constructs sub-base-alignment from the full alignment, delete all gaps mut_subalg = problem.subalignment.get_mutable_alignment() remaining_cols = mut_subalg.delete_all_gap() problem.annotations["ref.alignment.columns"] = remaining_cols print("num remaining_cols: ", len(remaining_cols)) problem.fragments = frags ap_alg = problem.read_extendend_alignment_and_relabel_columns(