def setUp(self):
"""Clearcut 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))
self.temp_dir = tempfile.mkdtemp()
# self.temp_dir_spaces = '/tmp/test for clearcut/'
# try:
# mkdir(self.temp_dir_spaces)
# except OSError:
# pass
try:
# create sequence files
f = open(path.join(self.temp_dir, "seq1.txt"), "w")
f.write("\n".join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, "seq2.txt"), "w")
g.write("\n".join(self.lines2))
g.close()
except OSError:
pass
def setUp(self):
"""Clearcut 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))
self.temp_dir = tempfile.mkdtemp()
#self.temp_dir_spaces = '/tmp/test for clearcut/'
#try:
# mkdir(self.temp_dir_spaces)
#except OSError:
# pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'),'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
def setUp(self):
"""Clearcut 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))
self.temp_dir = tempfile.mkdtemp()
#self.temp_dir_spaces = '/tmp/test for clearcut/'
#try:
# mkdir(self.temp_dir_spaces)
#except OSError:
# pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'), 'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'), 'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
def setUp(self):
"""Muscle general setUp method for all tests"""
# Check if muscle version is supported for this test
acceptable_version = (3, 6)
command = "muscle -version"
proc = Popen(command,shell=True,universal_newlines=True,\
stdout=PIPE,stderr=STDOUT)
stdout = proc.stdout.read()
version_string = stdout.strip().split(' ')[1].strip()[1:]
try:
version = tuple(map(int, version_string.split('.')))
pass_test = version[:2] == acceptable_version
except ValueError:
pass_test = False
version_string = stdout
self.assertTrue(pass_test,\
"Unsupported muscle version. %s is required, but running %s." \
% ('.'.join(map(str,acceptable_version)), version_string))
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))
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for muscle/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'), 'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'), 'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
def test_build_tree_from_alignment(self):
"""Clearcut should return a tree built from the passed alignment"""
tree_short = build_tree_from_alignment(build_tree_seqs_short,\
moltype=DNA)
num_seqs = flatten(build_tree_seqs_short).count('>')
self.assertEqual(len(tree_short.tips()), num_seqs)
tree_long = build_tree_from_alignment(build_tree_seqs_long, moltype=DNA)
seq_names = []
for line in 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()
#repeat with best_tree = True
tree_long = build_tree_from_alignment(build_tree_seqs_long,\
best_tree=True,\
moltype=DNA)
seq_names = []
for line in 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()
#build_tree_from_alignment should raise DataError when constructing
# an Alignment from unaligned sequences. Clearcut only allows aligned
# or a distance matrix as input.
self.assertRaises(DataError,build_tree_from_alignment,\
build_tree_seqs_unaligned,DNA)
def setUp(self):
"""Check if Raxml version is supported for this test"""
acceptable_version = (7,3,0)
self.assertTrue(app_path('raxmlHPC'),
"raxmlHPC not found. This may or may not be a problem depending on "+\
"which components of QIIME you plan to use.")
command = "raxmlHPC -v | grep version"
proc = Popen(command,shell=True,universal_newlines=True,\
stdout=PIPE,stderr=STDOUT)
stdout = proc.stdout.read()
version_string = stdout.strip().split(' ')[4].strip()
try:
version = tuple(map(int,version_string.split('.')))
pass_test = version == acceptable_version
except ValueError:
pass_test = False
version_string = stdout
self.assertTrue(pass_test,\
"Unsupported raxmlHPC version. %s is required, but running %s." \
% ('.'.join(map(str,acceptable_version)), version_string))
"""Setup data for raxml tests"""
self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC',
'GCGGCUAUUAGAUCGUA']
self.labels1 = ['>1','>2','>3']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.test_model = "GTRCAT"
self.align1 = get_align_for_phylip(StringIO(PHYLIP_FILE))
self.test_fn1 = "/tmp/raxml_test1.txt"
self.test_fn2 = "raxml_test1.txt"
self.test_fn1_space = "/tmp/raxml test1.txt"
def getDistinct(self, table_name, column):
"""returns the Ensembl data-bases distinct values for the named
property_type.
Arguments:
- table_name: the data base table name
- column: valid values are biotype, status"""
table = self.getTable(table_name)
query = sql.select([table.c[column]], distinct=True)
records = set()
string_types = str, unicode
for record in query.execute():
if type(record) not in string_types and \
type(record[0]) not in string_types:
# multi-dimensioned list/tuple
record = flatten(record)
elif type(record) not in string_types:
# list/tuple of strings
record = tuple(record)
else:
# a string
record = [record]
records.update(record)
return records
def getDistinct(self, table_name, column):
"""returns the Ensembl data-bases distinct values for the named
property_type.
Arguments:
- table_name: the data base table name
- column: valid values are biotype, status"""
table = self.getTable(table_name)
query = sql.select([table.c[column]], distinct=True)
records = set()
string_types = str, unicode
for record in query.execute():
if type(record) not in string_types and \
type(record[0]) not in string_types:
# multi-dimensioned list/tuple
record = flatten(record)
elif type(record) not in string_types:
# list/tuple of strings
record = tuple(record)
else:
# a string
record = [record]
records.update(record)
return records
def setUp(self):
"""Check if Raxml version is supported for this test"""
acceptable_version = (7, 3, 0)
self.assertTrue(app_path('raxmlHPC'),
"raxmlHPC not found. This may or may not be a problem depending on "+\
"which components of QIIME you plan to use.")
command = "raxmlHPC -v | grep version"
proc = Popen(command,shell=True,universal_newlines=True,\
stdout=PIPE,stderr=STDOUT)
stdout = proc.stdout.read()
version_string = stdout.strip().split(' ')[4].strip()
try:
version = tuple(map(int, version_string.split('.')))
pass_test = version == acceptable_version
except ValueError:
pass_test = False
version_string = stdout
self.assertTrue(pass_test,\
"Unsupported raxmlHPC version. %s is required, but running %s." \
% ('.'.join(map(str,acceptable_version)), version_string))
"""Setup data for raxml tests"""
self.seqs1 = [
'ACUGCUAGCUAGUAGCGUACGUA', 'GCUACGUAGCUAC', 'GCGGCUAUUAGAUCGUA'
]
self.labels1 = ['>1', '>2', '>3']
self.lines1 = flatten(zip(self.labels1, self.seqs1))
self.test_model = "GTRCAT"
self.align1 = get_align_for_phylip(StringIO(PHYLIP_FILE))
self.test_fn1 = "/tmp/raxml_test1.txt"
self.test_fn2 = "raxml_test1.txt"
self.test_fn1_space = "/tmp/raxml test1.txt"
def test_build_tree_from_alignment(self):
"""Clearcut should return a tree built from the passed alignment"""
tree_short = build_tree_from_alignment(build_tree_seqs_short,\
moltype=DNA)
num_seqs = flatten(build_tree_seqs_short).count('>')
self.assertEqual(len(tree_short.tips()), num_seqs)
tree_long = build_tree_from_alignment(build_tree_seqs_long,
moltype=DNA)
seq_names = []
for line in 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()
#repeat with best_tree = True
tree_long = build_tree_from_alignment(build_tree_seqs_long,\
best_tree=True,\
moltype=DNA)
seq_names = []
for line in 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()
#build_tree_from_alignment should raise DataError when constructing
# an Alignment from unaligned sequences. Clearcut only allows aligned
# or a distance matrix as input.
self.assertRaises(DataError,build_tree_from_alignment,\
build_tree_seqs_unaligned,DNA)
def setUp(self):
"""Muscle general setUp method for all tests"""
# Check if muscle version is supported for this test
acceptable_version = (3,6)
command = "muscle -version"
proc = Popen(command,shell=True,universal_newlines=True,\
stdout=PIPE,stderr=STDOUT)
stdout = proc.stdout.read()
version_string = stdout.strip().split(' ')[1].strip()[1:]
try:
version = tuple(map(int,version_string.split('.')))
pass_test = version[:2] == acceptable_version
except ValueError:
pass_test = False
version_string = stdout
self.assertTrue(pass_test,\
"Unsupported muscle version. %s is required, but running %s." \
% ('.'.join(map(str,acceptable_version)), version_string))
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))
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for muscle/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'),'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
def test_with_remainder(self):
"""return the correct groups when there's a remainder"""
data = range(21)
grouped = util.make_even_groups(data, 5)
self.assertEqual(len(grouped), 4)
for group in grouped:
self.assertEqual(len(group), 5)
full = sorted(flatten(grouped))
self.assertEqual(full, data[:-1])
def test_one_group(self):
"""only one group"""
data = range(20)
grouped = util.make_even_groups(data, 20)
self.assertEqual(len(grouped), 1)
for group in grouped:
self.assertEqual(len(group), 20)
full = sorted(flatten(grouped))
self.assertEqual(full, data)
def setUp(self):
"""Mafft 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.aligned1 = {'1': 'acugcuagcuaguagcguacgua',\
'2': 'gcuacguagcuac----------',\
'3': 'gcggcuauuagau------cgua',\
}
self.seqs2 = [
'UAGGCUCUGAUAUAAUAGCUCUC', 'UAUCGCUUCGACGAUUCUCUGAUAGAGA',
'UGACUACGCAU'
]
self.labels2 = ['>a', '>b', '>c']
self.lines2 = flatten(zip(self.labels2, self.seqs2))
self.aligned2 = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC---------',\
'b': 'UA----UCGCUUCGACGAUUCUCUGAUAGAGA',\
'c': 'UG------------ACUACGCAU---------',\
}
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for mafft/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'), 'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'), 'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
def setUp(self):
"""Mafft 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.aligned1 = {'1': 'acugcuagcuaguagcguacgua',\
'2': 'gcuacguagcuac----------',\
'3': 'gcggcuauuagau------cgua',\
}
self.seqs2=['UAGGCUCUGAUAUAAUAGCUCUC','UAUCGCUUCGACGAUUCUCUGAUAGAGA',
'UGACUACGCAU']
self.labels2=['>a','>b','>c']
self.lines2 = flatten(zip(self.labels2,self.seqs2))
self.aligned2 = {'a': 'UAGGCUCUGAUAUAAUAGCUCUC---------',\
'b': 'UA----UCGCUUCGACGAUUCUCUGAUAGAGA',\
'c': 'UG------------ACUACGCAU---------',\
}
self.temp_dir = tempfile.mkdtemp()
self.temp_dir_spaces = '/tmp/test for mafft/'
try:
mkdir(self.temp_dir_spaces)
except OSError:
pass
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
g = open(path.join(self.temp_dir, 'seq2.txt'),'w')
g.write('\n'.join(self.lines2))
g.close()
except OSError:
pass
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_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 setUp(self):
"""Setup data for raxml tests"""
self.seqs1 = ['ACUGCUAGCUAGUAGCGUACGUA','GCUACGUAGCUAC',
'GCGGCUAUUAGAUCGUA']
self.labels1 = ['>1','>2','>3']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.test_model = "GTRCAT"
self.align1 = get_align_for_phylip(StringIO(PHYLIP_FILE))
self.test_fn1 = "/tmp/raxml_test1.txt"
self.test_fn2 = "raxml_test1.txt"
self.test_fn1_space = "/tmp/raxml test1.txt"
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_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 setUp(self):
"""Setup data for raxml tests"""
self.seqs1 = [
'ACUGCUAGCUAGUAGCGUACGUA', 'GCUACGUAGCUAC', 'GCGGCUAUUAGAUCGUA'
]
self.labels1 = ['>1', '>2', '>3']
self.lines1 = flatten(zip(self.labels1, self.seqs1))
self.test_model = "GTRCAT"
self.align1 = get_align_for_phylip(StringIO(PHYLIP_FILE))
self.test_fn1 = "/tmp/raxml_test1.txt"
self.test_fn2 = "raxml_test1.txt"
self.test_fn1_space = "/tmp/raxml test1.txt"
def test_build_tree_from_alignment(self):
"""Muscle should return a tree built from the passed alignment"""
tree_short = build_tree_from_alignment(build_tree_seqs_short, DNA)
num_seqs = flatten(build_tree_seqs_short).count('>')
self.assertEqual(len(tree_short.tips()), num_seqs)
tree_long = build_tree_from_alignment(build_tree_seqs_long, DNA)
seq_names = []
for line in 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_build_tree_from_alignment(self):
"""Muscle should return a tree built from the passed alignment"""
tree_short = build_tree_from_alignment(build_tree_seqs_short, DNA)
num_seqs = flatten(build_tree_seqs_short).count('>')
self.assertEqual(len(tree_short.tips()), num_seqs)
tree_long = build_tree_from_alignment(build_tree_seqs_long, DNA)
seq_names = []
for line in 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 _get_symbol_from_synonym(self, db, synonym):
"""returns the gene symbol for a synonym"""
synonym_table = db.getTable("external_synonym")
xref_table = db.getTable("xref")
joinclause = xref_table.join(synonym_table, xref_table.c.xref_id == synonym_table.c.xref_id)
whereclause = synonym_table.c.synonym == synonym
query = sql.select([xref_table.c.display_label], from_obj=[joinclause], whereclause=whereclause).distinct()
result = query.execute().fetchall()
if result:
try:
symbol = flatten(result)[0]
except IndexError:
symbol = None
else:
symbol = None
return symbol
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)]
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)]
def _get_symbol_from_synonym(self, db, synonym):
"""returns the gene symbol for a synonym"""
synonym_table = db.getTable('external_synonym')
xref_table = db.getTable('xref')
joinclause = xref_table.join(
synonym_table, xref_table.c.xref_id == synonym_table.c.xref_id)
whereclause = synonym_table.c.synonym == synonym
query = sql.select([xref_table.c.display_label],
from_obj=[joinclause],
whereclause=whereclause).distinct()
result = query.execute().fetchall()
if result:
try:
symbol = flatten(result)[0]
except IndexError:
symbol = None
else:
symbol = None
return symbol
def seqids_from_otu_to_seqid(otu_to_seqid):
"""Returns set of all seq ids from libs"""
return set(flatten(otu_to_seqid.values()))
def make_mage_output(groups, colors, coord_header, coords, pct_var, \
background_color,label_color,data_colors, \
taxa=None, custom_axes=None,name='', \
radius=None, alpha=.75, num_coords=10,scaled=False, \
coord_scale=1.05, edges=None, coords_low=None, \
coords_high=None, ellipsoid_prefs=None,
user_supplied_edges=False, ball_scale=1.0, \
arrow_colors={'line_color': 'white', 'head_color': 'red'}):
"""Convert groups, colors, coords and percent var into mage format"""
result = []
#Scale the coords and generate header labels
if scaled:
scalars = pct_var
if custom_axes:
# create a dummy vector of ones to avoid scaling custom axes
custom_scalars = scalars[0] * np.ones(len(custom_axes))
scalars = np.append(custom_scalars,scalars)
coords = scale_pc_data_matrix(coords, scalars)
if not coords_low is None:
coords_low = scale_pc_data_matrix(coords_low, scalars)
if not coords_high is None:
coords_high = scale_pc_data_matrix(coords_high, scalars)
header_suffix = '_scaled'
else:
header_suffix = '_unscaled'
if radius is None:
radius = float(auto_radius(coords))*float(ball_scale)
else:
radius = float(radius)*float(ball_scale)
maxes = coords.max(0)[:num_coords]
mins = coords.min(0)[:num_coords]
pct_var = pct_var[:num_coords] #scale from fraction
#check that we didn't get fewer dimensions than we wanted
if len(mins) < num_coords:
num_coords = len(mins)
min_maxes = flatten(zip(mins,maxes))
if custom_axes:
axis_names = ['PC%s' %(i+1) for i in xrange(num_coords - len(custom_axes))]
axis_names = custom_axes + axis_names
else:
axis_names = ['PC%s' %(i+1) for i in xrange(num_coords)]
#Write the header information
result.append('@kinemage {%s}' % (name+header_suffix))
result.append('@dimension '+' '.join(['{%s}'%(name) for name in axis_names]))
result.append('@dimminmax '+ ' '.join(map(str, min_maxes)))
result.append('@master {points}')
result.append('@master {labels}')
if edges:
result.append('@master {edges}')
if not taxa is None:
result.append('@master {taxa_points}')
result.append('@master {taxa_labels}')
for name, color in sorted(data_colors.items()):
result.append(color.toMage())
if background_color=='white':
result.append('@whitebackground')
result.append('@hsvcolor {black} 0.0 0.0 0.0')
else:
result.append('@hsvcolor {white} 180.0 0.0 100.0')
#Write the groups, colors and coords
coord_dict = dict(zip(coord_header, coords))
if not coords_low is None:
coord_low_dict = dict(zip(coord_header, coords_low))
if not coords_high is None:
coord_high_dict = dict(zip(coord_header, coords_high))
for group_name in natsort(groups):
ids = groups[group_name]
result.append('@group {%s (n=%s)} collapsible' % (group_name, len(ids)))
color = colors[group_name]
coord_lines = []
for id_ in sorted(ids):
if id_ in coord_dict:
coord_lines.append('{%s} %s' % \
(id_, ' '.join(map(str, coord_dict[id_][:num_coords]))))
# create list of balls, one for each sample
result.append('@balllist color=%s radius=%s alpha=%s dimension=%s \
master={points} nobutton' % (color, radius, alpha, num_coords))
result.append('\n'.join(coord_lines))
# make ellipsoids if low and high coord bounds were received
if (not coords_low is None) and (not coords_high is None):
# create one trianglelist for each sample to define ellipsoids
result += make_mage_ellipsoids(ids, coord_dict, coord_low_dict,
coord_high_dict, color, ellipsoid_prefs)
# create list of labels
result.append('@labellist color=%s radius=%s alpha=%s dimension=%s \
master={labels} nobutton' % (color, radius, alpha, num_coords))
result.append('\n'.join(coord_lines))
if not taxa is None:
result += make_mage_taxa(taxa, num_coords, pct_var,
scaled=scaled, scalars=None, radius=radius)
#Write the axes on the bottom of the graph
result.append('@group {axes} collapsible')
state = 'on'
axis_mins = mins*coord_scale
axis_maxes = maxes*coord_scale
if not custom_axes:
custom_axes = []
# draw each axis
for i in xrange(num_coords):
if i == 3:
state = 'off'
result.append('@vectorlist {%s line} dimension=%s %s' % \
(axis_names[i], num_coords, state))
result.append(' '.join(map(str, axis_mins)) + ' ' + label_color)
end = axis_mins.copy()
end[i] = axis_maxes[i]
result.append(' '.join(map(str, end)) + ' ' + label_color)
end[i] *= coord_scale #add scale factor to offset labels a little
# custom axes come first, no "percent variance" shown
if i < len(custom_axes):
result.append('@labellist {%s} dimension=%s %s' % \
(axis_names[i], num_coords, state))
result.append( ('{%s}' % (axis_names[i])) + \
' '.join(map(str, end)) + ' ' + label_color)
# if all custom axes have been drawn, draw normal PC axes
else:
pct = pct_var[i-len(custom_axes)]
result.append('@labellist {%s (%0.2g%%)} dimension=%s %s' % \
(axis_names[i], pct, num_coords, state))
result.append( ('{%s (%0.2g%%)}' % (axis_names[i], pct)) + \
' '.join(map(str, end)) + ' ' + label_color)
#Write edges if requested
if edges:
result += make_edges_output(coord_dict, edges, num_coords, label_color,
arrow_colors=arrow_colors,
user_supplied_edges=user_supplied_edges)
return result
def make_mage_output(groups, colors, coord_header, coords, pct_var, \
background_color,label_color,data_colors, \
taxa=None, custom_axes=None,name='', \
radius=None, alpha=.75, num_coords=10,scaled=False, \
coord_scale=1.05, edges=None, coords_low=None, \
coords_high=None, ellipsoid_prefs=None,
user_supplied_edges=False):
"""Convert groups, colors, coords and percent var into mage format"""
result = []
#Scale the coords and generate header labels
if scaled:
scalars = pct_var
if custom_axes:
# create a dummy vector of ones to avoid scaling custom axes
custom_scalars = scalars[0] * np.ones(len(custom_axes))
scalars = np.append(custom_scalars, scalars)
coords = scale_pc_data_matrix(coords, scalars)
if not coords_low is None:
coords_low = scale_pc_data_matrix(coords_low, scalars)
if not coords_high is None:
coords_high = scale_pc_data_matrix(coords_high, scalars)
header_suffix = '_scaled'
else:
header_suffix = '_unscaled'
if radius is None:
radius = auto_radius(coords)
maxes = coords.max(0)[:num_coords]
mins = coords.min(0)[:num_coords]
pct_var = pct_var[:num_coords] #scale from fraction
#check that we didn't get fewer dimensions than we wanted
if len(mins) < num_coords:
num_coords = len(mins)
min_maxes = flatten(zip(mins, maxes))
if custom_axes:
axis_names = [
'PC%s' % (i + 1) for i in xrange(num_coords - len(custom_axes))
]
axis_names = custom_axes + axis_names
else:
axis_names = ['PC%s' % (i + 1) for i in xrange(num_coords)]
#Write the header information
result.append('@kinemage {%s}' % (name + header_suffix))
result.append('@dimension ' +
' '.join(['{%s}' % (name) for name in axis_names]))
result.append('@dimminmax ' + ' '.join(map(str, min_maxes)))
result.append('@master {points}')
result.append('@master {labels}')
if edges:
result.append('@master {edges}')
if not taxa is None:
result.append('@master {taxa_points}')
result.append('@master {taxa_labels}')
for name, color in sorted(data_colors.items()):
result.append(color.toMage())
if background_color == 'white':
result.append('@whitebackground')
result.append('@hsvcolor {black} 0.0 0.0 0.0')
else:
result.append('@hsvcolor {white} 180.0 0.0 100.0')
#Write the groups, colors and coords
coord_dict = dict(zip(coord_header, coords))
if not coords_low is None:
coord_low_dict = dict(zip(coord_header, coords_low))
if not coords_high is None:
coord_high_dict = dict(zip(coord_header, coords_high))
for group_name in natsort(groups):
ids = groups[group_name]
result.append('@group {%s (n=%s)} collapsible' %
(group_name, len(ids)))
color = colors[group_name]
coord_lines = []
for id_ in sorted(ids):
if id_ in coord_dict:
coord_lines.append('{%s} %s' % \
(id_, ' '.join(map(str, coord_dict[id_][:num_coords]))))
# create list of balls, one for each sample
result.append('@balllist color=%s radius=%s alpha=%s dimension=%s \
master={points} nobutton' % (color, radius, alpha, num_coords))
result.append('\n'.join(coord_lines))
# make ellipsoids if low and high coord bounds were received
if (not coords_low is None) and (not coords_high is None):
# create one trianglelist for each sample to define ellipsoids
result += make_mage_ellipsoids(ids, coord_dict, coord_low_dict,
coord_high_dict, color,
ellipsoid_prefs)
# create list of labels
result.append('@labellist color=%s radius=%s alpha=%s dimension=%s \
master={labels} nobutton' % (color, radius, alpha, num_coords))
result.append('\n'.join(coord_lines))
if not taxa is None:
result += make_mage_taxa(taxa,
num_coords,
pct_var,
scaled=scaled,
scalars=None,
radius=radius)
#Write the axes on the bottom of the graph
result.append('@group {axes} collapsible')
state = 'on'
axis_mins = mins * coord_scale
axis_maxes = maxes * coord_scale
if not custom_axes:
custom_axes = []
# draw each axis
for i in xrange(num_coords):
if i == 3:
state = 'off'
result.append('@vectorlist {%s line} dimension=%s %s' % \
(axis_names[i], num_coords, state))
result.append(' '.join(map(str, axis_mins)) + ' ' + label_color)
end = axis_mins.copy()
end[i] = axis_maxes[i]
result.append(' '.join(map(str, end)) + ' ' + label_color)
end[i] *= coord_scale #add scale factor to offset labels a little
# custom axes come first, no "percent variance" shown
if i < len(custom_axes):
result.append('@labellist {%s} dimension=%s %s' % \
(axis_names[i], num_coords, state))
result.append( ('{%s}' % (axis_names[i])) + \
' '.join(map(str, end)) + ' ' + label_color)
# if all custom axes have been drawn, draw normal PC axes
else:
pct = pct_var[i - len(custom_axes)]
result.append('@labellist {%s (%0.2g%%)} dimension=%s %s' % \
(axis_names[i], pct, num_coords, state))
result.append( ('{%s (%0.2g%%)}' % (axis_names[i], pct)) + \
' '.join(map(str, end)) + ' ' + label_color)
#Write edges if requested
if edges:
result += make_edges_output(coord_dict,
edges,
num_coords,
label_color,
user_supplied_edges=user_supplied_edges)
return result
def setUp(self):
"""Dialign general setUp method for all tests"""
self.seqs1 = ['LDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLRAAK',
'PDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALDAGTSAQRAELIALTQALKM',
'RPGLCQVFADATPTGWGLVMGHQRMRGTFSAPLPIHTAELLAACFARSRSGANIIGTDNSVV',
'MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIV']
self.labels1 = ['>HTL2','>MMLV', '>HEPB', '>ECOL']
self.lines1 = flatten(zip(self.labels1,self.seqs1))
self.out = \
"""
DIALIGN 2.2.1
*************
Program code written by Burkhard Morgenstern and Said Abdeddaim
e-mail contact: dialign (at) gobics (dot) de
Published research assisted by DIALIGN 2 should cite:
Burkhard Morgenstern (1999).
DIALIGN 2: improvement of the segment-to-segment
approach to multiple sequence alignment.
Bioinformatics 15, 211 - 218.
For more information, please visit the DIALIGN home page at
http://bibiserv.techfak.uni-bielefeld.de/dialign/
************************************************************
program call: dialign2-2 -fa -fn /tmp/di/seq1.fasta /tmp/di/seq1.txt
Aligned sequences: length:
================== =======
1) HTL2 57
2) MMLV 58
3) HEPB 62
4) ECOL 54
Average seq. length: 57.8
Please note that only upper-case letters are considered to be aligned.
Alignment (DIALIGN format):
===========================
HTL2 1 ldtapC-LFS DGS------P QKAAYVL--- ----WDQTIL QQDITPLPSH
MMLV 1 pdadhtw-YT DGSSLLQEGQ RKAGAAVtte teviWa---- KALDAG---T
HEPB 1 rpgl-CQVFA DAT------P TGWGLVM--- ----GHQRMR GTFSAPLPIH
ECOL 1 mlkqv-EIFT DGSCLGNPGP GGYGAIL--- ----RYRGRE KTFSAGytrT
0000000588 8882222229 9999999000 0000666666 6666633334
HTL2 37 ethSAQKGEL LALICGLRAa k--------- ---
MMLV 43 ---SAQRAEL IALTQALKm- ---------- ---
HEPB 37 t------AEL LAA-CFARSr sganiigtdn svv
ECOL 43 ---TNNRMEL MAAIv----- ---------- ---
0003333455 5533333300 0000000000 000
Sequence tree:
==============
Tree constructed using UPGMAbased on DIALIGN fragment weight scores
((HTL2 :0.130254MMLV :0.130254):0.067788(HEPB :0.120520ECOL :0.120520):0.077521);
"""
self.temp_dir = tempfile.mkdtemp()
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'),'w')
f.write('\n'.join(self.lines1))
f.close()
except OSError:
pass
def expand_otu_map_seq_ids(otu_map, seq_id_map):
for otu_id, seq_ids in otu_map.items():
mapped_seq_ids = flatten([seq_id_map[seq_id] for seq_id in seq_ids])
otu_map[otu_id] = mapped_seq_ids
return otu_map
def expand_otu_map_seq_ids(otu_map, seq_id_map):
for otu_id, seq_ids in otu_map.items():
mapped_seq_ids = flatten(\
[seq_id_map[seq_id] for seq_id in seq_ids])
otu_map[otu_id] = mapped_seq_ids
return otu_map
def setUp(self):
"""Dialign general setUp method for all tests"""
self.seqs1 = [
'LDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLRAAK',
'PDADHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALDAGTSAQRAELIALTQALKM',
'RPGLCQVFADATPTGWGLVMGHQRMRGTFSAPLPIHTAELLAACFARSRSGANIIGTDNSVV',
'MLKQVEIFTDGSCLGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIV'
]
self.labels1 = ['>HTL2', '>MMLV', '>HEPB', '>ECOL']
self.lines1 = flatten(zip(self.labels1, self.seqs1))
self.out = \
"""
DIALIGN 2.2.1
*************
Program code written by Burkhard Morgenstern and Said Abdeddaim
e-mail contact: dialign (at) gobics (dot) de
Published research assisted by DIALIGN 2 should cite:
Burkhard Morgenstern (1999).
DIALIGN 2: improvement of the segment-to-segment
approach to multiple sequence alignment.
Bioinformatics 15, 211 - 218.
For more information, please visit the DIALIGN home page at
http://bibiserv.techfak.uni-bielefeld.de/dialign/
************************************************************
program call: dialign2-2 -fa -fn /tmp/di/seq1.fasta /tmp/di/seq1.txt
Aligned sequences: length:
================== =======
1) HTL2 57
2) MMLV 58
3) HEPB 62
4) ECOL 54
Average seq. length: 57.8
Please note that only upper-case letters are considered to be aligned.
Alignment (DIALIGN format):
===========================
HTL2 1 ldtapC-LFS DGS------P QKAAYVL--- ----WDQTIL QQDITPLPSH
MMLV 1 pdadhtw-YT DGSSLLQEGQ RKAGAAVtte teviWa---- KALDAG---T
HEPB 1 rpgl-CQVFA DAT------P TGWGLVM--- ----GHQRMR GTFSAPLPIH
ECOL 1 mlkqv-EIFT DGSCLGNPGP GGYGAIL--- ----RYRGRE KTFSAGytrT
0000000588 8882222229 9999999000 0000666666 6666633334
HTL2 37 ethSAQKGEL LALICGLRAa k--------- ---
MMLV 43 ---SAQRAEL IALTQALKm- ---------- ---
HEPB 37 t------AEL LAA-CFARSr sganiigtdn svv
ECOL 43 ---TNNRMEL MAAIv----- ---------- ---
0003333455 5533333300 0000000000 000
Sequence tree:
==============
Tree constructed using UPGMAbased on DIALIGN fragment weight scores
((HTL2 :0.130254MMLV :0.130254):0.067788(HEPB :0.120520ECOL :0.120520):0.077521);
"""
self.temp_dir = tempfile.mkdtemp()
try:
#create sequence files
f = open(path.join(self.temp_dir, 'seq1.txt'), 'w')
f.write('\n'.join(self.lines1))
f.close()
except OSError:
pass
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
def Scores(self, value):
if not hasattr(self, '_probeset_scores'):
self._probeset_scores = None
self._probeset_scores = flatten(value)
def seqids_from_otu_to_seqid(otu_to_seqid):
"""Returns set of all seq ids from libs"""
return set(flatten(otu_to_seqid.values()))
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