#!/usr/bin/env python """Tests for application controller for ClustalW v1.83""" import re from os import getcwd, remove, rmdir, mkdir, path import shutil from cogent.core.alignment import Alignment from cogent.core.moltype import RNA from cogent.util.unit_test import TestCase, main from cogent.util.misc import flatten from cogent.app.clustalw import Clustalw, alignUnalignedSeqsFromFile,\ alignUnalignedSeqs, alignTwoAlignments, addSeqsToAlignment,\ buildTreeFromAlignment, build_tree_from_alignment, \ bootstrap_tree_from_alignment, align_unaligned_seqs, \ align_and_build_tree, add_seqs_to_alignment, align_two_alignments from cogent.parse.fasta import MinimalFastaParser __author__ = "Sandra Smit" __copyright__ = "Copyright 2007-2012, The Cogent Project" __credits__ = ["Sandra Smit", "Rob Knight", "Daniel McDonald",\ "Jeremy Widmann"] __license__ = "GPL" __version__ = "1.5.3" __maintainer__ = "Sandra Smit" __email__ = "sandra.smit@colorado.edu" __status__ = "Development" cw_vers = re.compile("CLUSTAL W [(]1\.8[1-3][.\d]*[)]") class GeneralSetUp(TestCase): def setUp(self): """Clustalw general setUp method for all tests""" self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC', 'GCGGCUAUUAGAUCGUA'] self.aln1_fasta = ALIGN1_FASTA self.labels1 = ['>1','>2','>3'] self.lines1 = flatten(zip(self.labels1,self.seqs1)) self.stdout1 = STDOUT1 self.aln1 = ALIGN1 self.dnd1 = DND1 self.multiline1 = '\n'.join(flatten(zip(self.labels1, self.seqs1))) self.seqs2=['UAGGCUCUGAUAUAAUAGCUCUC','UAUCGCUUCGACGAUUCUCUGAUAGAGA', 'UGACUACGCAU'] self.labels2=['>a','>b','>c'] self.lines2 = flatten(zip(self.labels2,self.seqs2)) self.aln2 = ALIGN2 self.dnd2 = DND2 self.twoalign = TWOALIGN self.alignseqs = ALIGNSEQS self.treeduringalignseqs = TREEDURINGALIGNSEQS self.treefromalignseqs = TREEFROMALIGNSEQS self.temp_dir_space = "/tmp/clustalw test" self.build_tree_seqs_short = """>clustal_test_seqs_0 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT AGCTTTAAATCATGCCAGTG >clustal_test_seqs_1 GACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT TGCTTTCAATAATGCCAGTG >clustal_test_seqs_2 AACCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT TGCTTTGAATCATGCCAGTA >clustal_test_seqs_3 AAACCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT TGCTTTACATCATGCAAGTG >clustal_test_seqs_4 AACCGCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT TGCTTTAAATCATGCCAGTG >clustal_test_seqs_5 AACCCCCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA TGCTTTAAATCATGCCAGTT >clustal_test_seqs_6 GACCCCCGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT TACTTTAGATCATGCCGGTG >clustal_test_seqs_7 AACCCCCACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT TGCTTTAAATCATGCCAGTG >clustal_test_seqs_8 AACCCCCACGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT TGCATTAAATCATGCCAGTG >clustal_test_seqs_9 AAGCCCCACGGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA TGCTTTAAATCCTGACAGCG """ self.build_tree_seqs_long = """>clustal_test_seqs_0 AACCCCCACGGTGGATGCCACACGCCCCATACAAAGGGTAGGATGCTTAAGACACATCGCGTCAGGTTTGTGTCAGGCCT AGCTTTAAATCATGCCAGTG >clustal_test_seqsaaaaaaaa_1 GACCCACACGGTGGATGCAACAGATCCCATACACCGAGTTGGATGCTTAAGACGCATCGCGTGAGTTTTGCGTCAAGGCT TGCTTTCAATAATGCCAGTG >clustal_test_seqsaaaaaaaa_2 AACCCCCACGGTGGCAGCAACACGTCACATACAACGGGTTGGATTCTAAAGACAAACCGCGTCAAAGTTGTGTCAGAACT TGCTTTGAATCATGCCAGTA >clustal_test_seqsaaaaaaaa_3 AAACCCCACGGTAGCTGCAACACGTCCCATACCACGGGTAGGATGCTAAAGACACATCGGGTCTGTTTTGTGTCAGGGCT TGCTTTACATCATGCAAGTG >clustal_test_seqsaaaaaaaa_4 AACCGCCACGGTGGGTACAACACGTCCACTACATCGGCTTGGAAGGTAAAGACACGTCGCGTCAGTATTGCGTCAGGGCT TGCTTTAAATCATGCCAGTG >clustal_test_seqsaaaaaaaa_5 AACCCCCGCGGTAGGTGCAACACGTCCCATACAACGGGTTGGAAGGTTAAGACACAACGCGTTAATTTTGTGTCAGGGCA TGCTTTAAATCATGCCAGTT >clustal_test_seqsaaaaaaaa_6 GACCCCCGCGGTGGCTGCAAGACGTCCCATACAACGGGTTGGATGCTTAAGACACATCGCAACAGTTTTGAGTCAGGGCT TACTTTAGATCATGCCGGTG >clustal_test_seqsaaaaaaaa_7 AACCCCCACGGTGGCTACAAGACGTCCCATCCAACGGGTTGGATACTTAAGGCACATCACGTCAGTTTTGTGTCAGAGCT TGCTTTAAATCATGCCAGTG >clustal_test_seqsaaaaaaaa_8 AACCCCCACGGTGGCTGCAACACGTGGCATACAACGGGTTGGATGCTTAAGACACATCGCCTCAGTTTTGTGTCAGGGCT TGCATTAAATCATGCCAGTG >clustal_test_seqsaaaaaaaa_9 AAGCCCCACGGTGGCTGAAACACATCCCATACAACGGGTTGGATGCTTAAGACACATCGCATCAGTTTTATGTCAGGGGA TGCTTTAAATCCTGACAGCG """ try: mkdir('/tmp/ct') except OSError: #dir already exists pass try: #create sequence files f = open('/tmp/ct/seq1.txt','w') f.write('\n'.join(self.lines1)) f.close() g = open('/tmp/ct/seq2.txt','w') g.write('\n'.join(self.lines2)) g.close() #create alignment files f = open('/tmp/ct/align1','w') f.write(self.aln1) f.close() g = open('/tmp/ct/align2','w') g.write(self.aln2) g.close() #create tree file f = open('/tmp/ct/tree1','w') f.write(DND1) f.close() except OSError: pass class ClustalwTests(GeneralSetUp): """Tests for the Clustalw application controller""" def test_base_command(self): """Clustalw BaseCommand should return the correct BaseCommand""" c = Clustalw() self.assertEqual(c.BaseCommand,\ ''.join(['cd "',getcwd(),'/"; ','clustalw -align'])) c.Parameters['-infile'].on('seq.txt') self.assertEqual(c.BaseCommand,\ ''.join(['cd "',getcwd(),'/"; ',\ 'clustalw -infile="seq.txt" -align'])) c.Parameters['-align'].off() self.assertEqual(c.BaseCommand,\ ''.join(['cd "',getcwd(),'/"; ','clustalw -infile="seq.txt"'])) c.Parameters['-nopgap'].on() c.Parameters['-infile'].off() self.assertEqual(c.BaseCommand,\ ''.join(['cd "',getcwd(),'/"; ','clustalw -nopgap'])) def test_changing_working_dir(self): """Clustalw BaseCommand should change according to WorkingDir""" c = Clustalw(WorkingDir='/tmp/clustaltest') self.assertEqual(c.BaseCommand,\ ''.join(['cd "','/tmp/clustaltest','/"; ','clustalw -align'])) c = Clustalw(WorkingDir='/tmp/clustaltest/') self.assertEqual(c.BaseCommand,\ ''.join(['cd "','/tmp/clustaltest/','/"; ','clustalw -align'])) c = Clustalw() c.WorkingDir = '/tmp/clustaltest2/' self.assertEqual(c.BaseCommand,\ ''.join(['cd "','/tmp/clustaltest2/','/"; ','clustalw -align'])) #removing the dirs is proof that they were created at the same time #if the dirs are not there, an OSError will be raised rmdir('/tmp/clustaltest') rmdir('/tmp/clustaltest2') def test_stdout_input_as_string(self): """Clustalw input_as_string shoud function as expected""" c = Clustalw(WorkingDir='/tmp/ct') res = c('/tmp/ct/seq1.txt') self.assertEqual(cw_vers.sub("", res['StdOut'].read()), cw_vers.sub("", self.stdout1)) self.assertEqual(res['StdErr'].read(),'') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() def test_stdout_input_as_lines(self): """Clustalw input_as_lines should function as expected""" c = Clustalw(InputHandler='_input_as_lines',WorkingDir='/tmp/ct') res = c(self.lines1) #get info on input file name and change output accordingly name = c.Parameters['-infile'].Value out = self.stdout1.split('\n') out[16] =\ 'Guide tree file created: ['+name.rsplit(".")[0]+'.dnd]' out[23] =\ 'CLUSTAL-Alignment file created ['+name.rsplit(".")[0]+'.aln]' self.assertEqual(cw_vers.sub("", res['StdOut'].read()), cw_vers.sub("", '\n'.join(out))) self.assertEqual(res['StdErr'].read(),'') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() def test_stdout_input_as_lines_local(self): """Clustalw input_as_lines should function as expected""" c = Clustalw(InputHandler='_input_as_lines',WorkingDir=self.temp_dir_space) res = c(self.lines1) #get info on input file name and change output accordingly name = c.Parameters['-infile'].Value out = self.stdout1.split('\n') out[16] =\ 'Guide tree file created: ['+name.rsplit(".")[0]+'.dnd]' out[23] =\ 'CLUSTAL-Alignment file created ['+name.rsplit(".")[0]+'.aln]' self.assertEqual(cw_vers.sub("", res['StdOut'].read()), cw_vers.sub("", '\n'.join(out))) self.assertEqual(res['StdErr'].read(),'') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() def test_stdout_input_as_seqs(self): """Clustalw input_as_seqs should function as expected""" c = Clustalw(InputHandler='_input_as_seqs',WorkingDir='/tmp/ct') res = c(self.seqs1) #get info on input file name and change output accordingly name = c.Parameters['-infile'].Value out = self.stdout1.split('\n') out[16] =\ 'Guide tree file created: ['+name.rsplit(".")[0]+'.dnd]' out[23] =\ 'CLUSTAL-Alignment file created ['+name.rsplit(".")[0]+'.aln]' self.assertEqual(cw_vers.sub("", res['StdOut'].read()), cw_vers.sub("", '\n'.join(out))) self.assertEqual(res['StdErr'].read(),'') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() def test_stdout_input_as_multiline_string(self): """Clustalw input_as_multiline_string should function as expected""" c = Clustalw(InputHandler='_input_as_multiline_string',\ WorkingDir='/tmp/ct') res = c(self.multiline1) name = c.Parameters['-infile'].Value out = self.stdout1.split('\n') out[16] =\ 'Guide tree file created: ['+name.rsplit(".")[0]+'.dnd]' out[23] =\ 'CLUSTAL-Alignment file created ['+name.rsplit(".")[0]+'.aln]' self.assertEqual(cw_vers.sub("", res['StdOut'].read()), cw_vers.sub("", '\n'.join(out))) self.assertEqual(res['StdErr'].read(),'') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() def test_alignment_trees(self): """Clustalw alignment should work correctly with new/usetree""" c = Clustalw(params={'-quicktree':True,'-type':'DNA','-gapopen':10},\ WorkingDir='/tmp/ct') res = c('/tmp/ct/seq1.txt') self.assertEqual(res['Align'].name,'/tmp/ct/seq1.aln') self.assertEqual(res['Dendro'].name,'/tmp/ct/seq1.dnd') res.cleanUp() c.Parameters['-usetree'].on('/tmp/ct/tree1') c.Parameters['-output'].on('PHYLIP') res = c('/tmp/ct/seq1.txt') self.assertEqual(res['Align'].name,'/tmp/ct/seq1.phy') self.assertEqual(res['Dendro'].name,'/tmp/ct/tree1') res.cleanUp() c.Parameters['-newtree'].on('newtree') c.Parameters['-outfile'].on('outfile') res = c('/tmp/ct/seq1.txt') self.assertEqual(res['Align'].name, c.WorkingDir + 'outfile') self.assertEqual(res['Dendro'].name, c.WorkingDir + 'newtree') res.cleanUp() def test_profile_newtree(self): """Clustalw profile should work correctly with new/usetree""" c = Clustalw(params={'-profile':None,'-profile1':'/tmp/ct/seq1.txt',\ '-profile2':'/tmp/ct/seq2.txt','-newtree1':'lala'},\ WorkingDir='/tmp/ct') c.Parameters['-align'].off() res = c() self.assertEqual(res['Align'],None) self.assertEqual(res['Dendro1'].name,'/tmp/ct/lala') self.assertEqual(res['Dendro2'].name,'/tmp/ct/seq2.dnd') res.cleanUp() def test_sequences_newtree(self): """Clustalw sequences should work correctly with new/usetree""" c = Clustalw(params={'-sequences':None,'-newtree':'lala',\ '-profile1':'/tmp/ct/align1','-profile2':'/tmp/ct/seq2.txt'},\ WorkingDir='/tmp/ct') c.Parameters['-align'].off() res = c() self.assertEqual(res['Align'],None) self.assertEqual(res['Dendro'].name,'/tmp/ct/lala') res.cleanUp() #is this a bug in clustal. It's creating an empty file 'seq2.aln' #but doesn't report it in the stdout remove('/tmp/ct/seq2.aln') def test_tree_outputtree(self): """Clustalw tree should work correctly with outputtree""" c = Clustalw(params={'-tree':None,'-outputtree':'dist',\ '-infile':'/tmp/ct/align1'},WorkingDir='/tmp/ct/') c.Parameters['-align'].off() res = c() self.assertEqual(res['Tree'].name,'/tmp/ct/align1.ph') self.assertEqual(res['TreeInfo'].name,'/tmp/ct/align1.dst') res.cleanUp() class clustalwTests(GeneralSetUp): """Tests for module level functions in clustalw.py""" def test_alignUnalignedSeqs(self): """Clustalw alignUnalignedSeqs should work as expected""" res = alignUnalignedSeqs(self.seqs1,WorkingDir='/tmp/ct') self.assertNotEqual(res['StdErr'],None) self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() #suppress stderr and stdout res = alignUnalignedSeqs(self.seqs1,WorkingDir='/tmp/ct',\ SuppressStderr=True,SuppressStdout=True) self.assertEqual(res['StdOut'],None) self.assertEqual(res['StdErr'],None) self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() def test_alignUnalignedSeqsFromFile(self): """Clustalw alignUnalignedSeqsFromFile should work as expected""" #make temp file res = alignUnalignedSeqsFromFile('/tmp/ct/seq1.txt') self.assertEqual(cw_vers.sub("", res['StdOut'].read()), cw_vers.sub("", self.stdout1)) self.assertEqual(res['StdErr'].read(),'') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() #suppress stderr and stdout res = alignUnalignedSeqsFromFile('/tmp/ct/seq1.txt',\ SuppressStderr=True, SuppressStdout=True) self.assertEqual(res['StdOut'],None) self.assertEqual(res['StdErr'],None) self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.aln1)) self.assertEqual(res['Dendro'].read(),self.dnd1) res.cleanUp() def test_alignTwoAlignments(self): """Clustalw alignTwoAlignments should work as expected""" res = alignTwoAlignments('/tmp/ct/align1','/tmp/ct/align2',\ 'twoalign.aln') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.twoalign)) self.assertNotEqual(res['Dendro1'],None) self.assertNotEqual(res['Dendro2'],None) #are there new trees created during the profiling? #the produced trees are not the same as when aligning individually #self.assertEqual(res['Dendro1'].read(),self.dnd) #self.assertEqual(res['Dendro2'].read(),self.dnd2) res.cleanUp() def test_addSeqsToAlignment(self): """Clustalw addSeqsToAlignment shoudl work as expected""" res = addSeqsToAlignment('/tmp/ct/align1','/tmp/ct/seq2.txt',\ 'alignseqs') self.assertEqual(cw_vers.sub("", res['Align'].read()), cw_vers.sub("", self.alignseqs)) self.assertEqual(res['Dendro'].read(),self.treeduringalignseqs) res.cleanUp() def test_buildTreeFromAlignment(self): """Clustalw buildTreeFromAlignment shoudl work as expected""" pre_res = addSeqsToAlignment('/tmp/ct/align1','/tmp/ct/seq2.txt',\ 'alignseqs',WorkingDir='/tmp/ct') res = buildTreeFromAlignment('/tmp/ct/alignseqs',WorkingDir='/tmp/ct') self.assertEqual(res['Tree'].read(),self.treefromalignseqs) res.cleanUp() pre_res.cleanUp() def test_build_tree_from_alignment(self): """Clustalw should return a tree built from the passed alignment""" tree_short = build_tree_from_alignment(self.build_tree_seqs_short, \ RNA, best_tree=False) num_seqs = flatten(self.build_tree_seqs_short).count('>') self.assertEqual(len(tree_short.tips()), num_seqs) tree_long = build_tree_from_alignment(self.build_tree_seqs_long, \ RNA, best_tree=False) seq_names = [] for line in self.build_tree_seqs_long.split('\n'): if line.startswith('>'): seq_names.append(line[1:]) for node in tree_long.tips(): if node.Name not in seq_names: self.fail() tree_short = build_tree_from_alignment(self.build_tree_seqs_short, \ RNA, best_tree=True, params={'-bootstrap':3}) num_seqs = flatten(self.build_tree_seqs_short).count('>') self.assertEqual(len(tree_short.tips()), num_seqs) def test_align_unaligned_seqs(self): """Clustalw align_unaligned_seqs should work as expected""" res = align_unaligned_seqs(self.seqs1, RNA) self.assertEqual(res.toFasta(), self.aln1_fasta) def test_bootstrap_tree_from_alignment(self): """Clustalw should return a bootstrapped tree from the passed aln""" tree_short = bootstrap_tree_from_alignment(self.build_tree_seqs_short) num_seqs = flatten(self.build_tree_seqs_short).count('>') self.assertEqual(len(tree_short.tips()), num_seqs) tree_long = bootstrap_tree_from_alignment(self.build_tree_seqs_long) seq_names = [] for line in self.build_tree_seqs_long.split('\n'): if line.startswith('>'): seq_names.append(line[1:]) for node in tree_long.tips(): if node.Name not in seq_names: self.fail() def test_align_and_build_tree(self): """Aligns and builds a tree for a set of sequences""" res = align_and_build_tree(self.seqs1, RNA) self.assertEqual(res['Align'].toFasta(), self.aln1_fasta) tree = res['Tree'] seq_names = [] for line in self.aln1_fasta.split('\n'): if line.startswith('>'): seq_names.append(line[1:]) for node in tree.tips(): if node.Name not in seq_names: self.fail() def test_add_seqs_to_alignment(self): """Clustalw add_seqs_to_alignment should work as expected.""" seq2 = dict(MinimalFastaParser(self.lines2)) align1 = dict(MinimalFastaParser(ALIGN1_FASTA.split('\n'))) res = add_seqs_to_alignment(seq2,align1,RNA) self.assertEqual(res.toFasta(), SEQ_PROFILE_ALIGN) def test_align_two_alignments(self): """Clustalw align_two_alignments should work as expected.""" align1 = dict(MinimalFastaParser(ALIGN1_FASTA.split('\n'))) align2 = dict(MinimalFastaParser(ALIGN2_FASTA.split('\n'))) res = align_two_alignments(align1,align2,RNA) self.assertEqual(res.toFasta(), PROFILE_PROFILE_ALIGN) def test_zzz_general_cleanUp(self): """Last test executed: cleans up all files initially created""" remove('/tmp/ct/seq1.txt') remove('/tmp/ct/seq2.txt') remove('/tmp/ct/align1') remove('/tmp/ct/align2') remove('/tmp/ct/tree1') rmdir('/tmp/ct') shutil.rmtree(self.temp_dir_space) STDOUT1=\ """ CLUSTAL W (1.83) Multiple Sequence Alignments Sequence format is Pearson Sequence 1: 1 23 bp Sequence 2: 2 13 bp Sequence 3: 3 17 bp Start of Pairwise alignments Aligning... Sequences (1:2) Aligned. Score: 46 Sequences (1:3) Aligned. Score: 41 Sequences (2:3) Aligned. Score: 30 Guide tree file created: [/tmp/ct/seq1.dnd] Start of Multiple Alignment There are 2 groups Aligning... Group 1: Sequences: 2 Score:171 Group 2: Sequences: 3 Score:162 Alignment Score 33 CLUSTAL-Alignment file created [/tmp/ct/seq1.aln] """ ALIGN1=\ """CLUSTAL W (1.83) multiple sequence alignment 1 ACUGCUAGCUAGUAGCGUACGUA 2 ---GCUACGUAGCUAC------- 3 GCGGCUAUUAGAUCGUA------ **** """ ALIGN1_FASTA = ">seq_0\nACUGCUAGCUAGUAGCGUACGUA\n>seq_1\n---GCUACGUAGCUAC-------\n>seq_2\nGCGGCUAUUAGAUCGUA------" DND1=\ """( 1:0.21719, 2:0.32127, 3:0.37104); """ ALIGN2 =\ """CLUSTAL W (1.83) multiple sequence alignment a UAGGCUCUGAUAUAAUAGCUCUC--------- b ----UAUCGCUUCGACGAUUCUCUGAUAGAGA c ------------UGACUACGCAU--------- * * """ ALIGN2_FASTA = ">a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\n----UAUCGCUUCGACGAUUCUCUGAUAGAGA\n>c\n------------UGACUACGCAU---------" DND2=\ """( a:0.30435, b:0.30435, c:0.33202); """ TWOALIGN=\ """CLUSTAL W (1.83) multiple sequence alignment 1 ---ACUGCUAGCUAGUAGCGUACGUA------ 2 ------GCUACGUAGCUAC------------- 3 ---GCGGCUAUUAGAUCGUA------------ a UAGGCUCUGAUAUAAUAGCUCUC--------- b ----UAUCGCUUCGACGAUUCUCUGAUAGAGA c ------------UGACUACGCAU--------- """ ALIGNSEQS=\ """CLUSTAL W (1.83) multiple sequence alignment 1 ----------ACUGCUAGCUAGUAGCGUACGUA 2 -------------GCUACGUAGCUAC------- 3 ----------GCGGCUAUUAGAUCGUA------ a -------UAGGCUCUGAUAUAAUAGCUCUC--- c -------------------UGACUACGCAU--- b UAUCGCUUCGACGAUUCUCUGAUAGAGA----- """ TREEDURINGALIGNSEQS=\ """( 1:0.34511, ( 2:0.25283, ( ( 3:0.21486, a:0.19691) :0.11084, b:0.31115) :0.06785) :0.02780, c:0.20035); """ TREEFROMALIGNSEQS=\ """( ( ( 1:0.17223, ( 2:0.14749, c:0.13822) :0.19541) :0.07161, a:0.25531) :0.03600, 3:0.29438, b:0.23503); """ SEQ_PROFILE_ALIGN = """>a\n-------UAGGCUCUGAUAUAAUAGCUCUC---\n>b\nUAUCGCUUCGACGAUUCUCUGAUAGAGA-----\n>c\n-------------------UGACUACGCAU---\n>seq_0\n----------ACUGCUAGCUAGUAGCGUACGUA\n>seq_1\n-------------GCUACGUAGCUAC-------\n>seq_2\n----------GCGGCUAUUAGAUCGUA------""" PROFILE_PROFILE_ALIGN = """>a\nUAGGCUCUGAUAUAAUAGCUCUC---------\n>b\n----UAUCGCUUCGACGAUUCUCUGAUAGAGA\n>c\n------------UGACUACGCAU---------\n>seq_0\n---ACUGCUAGCUAGUAGCGUACGUA------\n>seq_1\n------GCUACGUAGCUAC-------------\n>seq_2\n---GCGGCUAUUAGAUCGUA------------""" if __name__ == '__main__': main()