def setUp(self): """Muscle general setUp method for all tests""" self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC', 'GCGGCUAUUAGAUCGUA'] self.labels1 = ['>1','>2','>3'] self.lines1 = flatten(zip(self.labels1,self.seqs1)) self.seqs2=['UAGGCUCUGAUAUAAUAGCUCUC','UAUCGCUUCGACGAUUCUCUGAUAGAGA', 'UGACUACGCAU'] self.labels2=['>a','>b','>c'] self.lines2 = flatten(zip(self.labels2,self.seqs2)) 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() except OSError: pass
def setUp(self): """Clustalw general setUp method for all tests""" self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC', 'GCGGCUAUUAGAUCGUA'] self.labels1 = ['>1','>2','>3'] self.lines1 = flatten(zip(self.labels1,self.seqs1)) self.stdout1 = STDOUT1 self.aln1 = ALIGN1 self.dnd1 = DND1 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 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
def extract(self, seq): """Returns bases in pairs as list of tuples. Note: always returns list, even if only one base pair. """ if self.Length > 1: return flatten([p.extract(seq) for p in self]) else: if self.Start is not None: start = seq[self.Start] else: start = None if self.End is not None: end = seq[self.End] else: end = None return [(start, end)]