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)]
