def test_get_align(self):
"""get_align_for_phylip should return Aligment object for phylip files"""
align = get_align_for_phylip(self.big_interleaved)
align = get_align_for_phylip(self.interleaved_little)
s = str(align)
self.assertEqual(s, '''>Archaeopt
CGATGCTTACCGCCGATGCTTACCGCCGATGCTTACCGC
>Hesperorni
CGTTACTCGTTGTCGTTACTCGTTGTCGTTACTCGTTGT
>Baluchithe
TAATGTTAATTGTTAATGTTAATTGTTAATGTTAATTGT
>B. virgini
TAATGTTCGTTGTTAATGTTCGTTGTTAATGTTCGTTGT
>Brontosaur
CAAAACCCATCATCAAAACCCATCATCAAAACCCATCAT
>B.subtilis
GGCAGCCAATCACGGCAGCCAATCACGGCAGCCAATCAC
''')
align = get_align_for_phylip(self.noninterleaved_little)
s = str(align)
self.assertEqual(s, '''>Archaeopt
CGATGCTTACCGCCGATGCT
>Hesperorni
CGTTACTCGTTGTCGTTACT
>Baluchithe
TAATGTTAATTGTTAATGTT
>B. virgini
TAATGTTCGTTGTTAATGTT
>Brontosaur
CAAAACCCATCATCAAAACC
>B.subtilis
GGCAGCCAATCACGGCAGCC
''')
def test_get_align(self):
"""get_align_for_phylip should return Aligment object for phylip files"""
align = get_align_for_phylip(self.big_interleaved)
align = get_align_for_phylip(self.interleaved_little)
s = str(align)
self.assertEqual(s, '''>Archaeopt
CGATGCTTACCGCCGATGCTTACCGCCGATGCTTACCGC
>Hesperorni
CGTTACTCGTTGTCGTTACTCGTTGTCGTTACTCGTTGT
>Baluchithe
TAATGTTAATTGTTAATGTTAATTGTTAATGTTAATTGT
>B. virgini
TAATGTTCGTTGTTAATGTTCGTTGTTAATGTTCGTTGT
>Brontosaur
CAAAACCCATCATCAAAACCCATCATCAAAACCCATCAT
>B.subtilis
GGCAGCCAATCACGGCAGCCAATCACGGCAGCCAATCAC
''')
align = get_align_for_phylip(self.noninterleaved_little)
s = str(align)
self.assertEqual(s, '''>Archaeopt
CGATGCTTACCGCCGATGCT
>Hesperorni
CGTTACTCGTTGTCGTTACT
>Baluchithe
TAATGTTAATTGTTAATGTT
>B. virgini
TAATGTTCGTTGTTAATGTT
>Brontosaur
CAAAACCCATCATCAAAACC
>B.subtilis
GGCAGCCAATCACGGCAGCC
''')
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 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 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 insert_sequences_into_tree(aln, moltype, params={},
write_log=True):
"""Returns a tree from Alignment object aln.
aln: an xxx.Alignment object, or data that can be used to build one.
moltype: cogent.core.moltype.MolType object
params: dict of parameters to pass in to the RAxML app controller.
The result will be an xxx.Alignment object, or None if tree fails.
"""
# convert aln to phy since seq_names need fixed to run through pplacer
new_aln=get_align_for_phylip(StringIO(aln))
# convert aln to fasta in case it is not already a fasta file
aln2 = Alignment(new_aln)
seqs = aln2.toFasta()
ih = '_input_as_multiline_string'
pplacer_app = Pplacer(params=params,
InputHandler=ih,
WorkingDir=None,
SuppressStderr=False,
SuppressStdout=False)
pplacer_result = pplacer_app(seqs)
# write a log file
if write_log:
log_fp = join(params["--out-dir"],'log_pplacer_' + \
split(get_tmp_filename())[-1])
log_file=open(log_fp,'w')
log_file.write(pplacer_result['StdOut'].read())
log_file.close()
# use guppy to convert json file into a placement tree
guppy_params={'tog':None}
new_tree=build_tree_from_json_using_params(pplacer_result['json'].name, \
output_dir=params['--out-dir'], \
params=guppy_params)
pplacer_result.cleanUp()
return new_tree
def insert_sequences_into_tree(aln, moltype, params={},
write_log=True):
"""Returns a tree from Alignment object aln.
aln: an xxx.Alignment object, or data that can be used to build one.
moltype: cogent.core.moltype.MolType object
params: dict of parameters to pass in to the RAxML app controller.
The result will be an xxx.Alignment object, or None if tree fails.
"""
# convert aln to phy since seq_names need fixed to run through pplacer
new_aln=get_align_for_phylip(StringIO(aln))
# convert aln to fasta in case it is not already a fasta file
aln2 = Alignment(new_aln)
seqs = aln2.toFasta()
ih = '_input_as_multiline_string'
pplacer_app = Pplacer(params=params,
InputHandler=ih,
WorkingDir=None,
SuppressStderr=False,
SuppressStdout=False)
pplacer_result = pplacer_app(seqs)
# write a log file
if write_log:
log_fp = join(params["--out-dir"],'log_pplacer_' + \
split(get_tmp_filename())[-1])
log_file=open(log_fp,'w')
log_file.write(pplacer_result['StdOut'].read())
log_file.close()
# use guppy to convert json file into a placement tree
guppy_params={'tog':None}
new_tree=build_tree_from_json_using_params(pplacer_result['json'].name, \
output_dir=params['--out-dir'], \
params=guppy_params)
pplacer_result.cleanUp()
return new_tree
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_insert_sequences_into_tree(self):
"""Inserts sequences into Tree using params - test handles tree-insertion"""
# generate temp filename for output
outfname = splitext(get_tmp_filename('/tmp/'))[0]
# create starting tree
outtreefname = outfname + '.tre'
outtree = open(outtreefname, 'w')
outtree.write(REF_TREE)
outtree.close()
# set params for tree-insertion
params = {}
params["-w"] = "/tmp/"
params["-n"] = get_tmp_filename().split("/")[-1]
params["-f"] = 'v'
#params["-G"] = '0.25'
params["-t"] = outtreefname
params["-m"] = 'GTRGAMMA'
aln_ref_query = get_align_for_phylip(
StringIO(PHYLIP_FILE_DNA_REF_QUERY))
aln = Alignment(aln_ref_query)
seqs, align_map = aln.toPhylip()
tree = insert_sequences_into_tree(seqs,
DNA,
params=params,
write_log=False)
for node in tree.tips():
removed_query_str = re.sub('QUERY___', '', str(node.Name))
new_node_name = re.sub('___\d+', '', str(removed_query_str))
if new_node_name in align_map:
node.Name = align_map[new_node_name]
self.assertTrue(isinstance(tree, PhyloNode))
self.assertEqual(tree.getNewick(with_distances=True), RESULT_TREE)
self.assertEqual(len(tree.tips()), 7)
self.assertRaises(NotImplementedError, build_tree_from_alignment, \
self.align1, RNA, True)
remove(outtreefname)
def insert_sequences_into_tree(aln, moltype, params={}):
"""Returns a tree from placement of sequences
"""
# convert aln to phy since seq_names need fixed to run through parsinsert
new_aln=get_align_for_phylip(StringIO(aln))
# convert aln to fasta in case it is not already a fasta file
aln2 = Alignment(new_aln)
seqs = aln2.toFasta()
parsinsert_app = ParsInsert(params=params)
result = parsinsert_app(seqs)
# parse tree
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
# cleanup files
result.cleanUp()
return tree
def insert_sequences_into_tree(aln, moltype, params={}):
"""Returns a tree from placement of sequences
"""
# convert aln to phy since seq_names need fixed to run through parsinsert
new_aln = get_align_for_phylip(StringIO(aln))
# convert aln to fasta in case it is not already a fasta file
aln2 = Alignment(new_aln)
seqs = aln2.toFasta()
parsinsert_app = ParsInsert(params=params)
result = parsinsert_app(seqs)
# parse tree
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
# cleanup files
result.cleanUp()
return tree
def test_insert_sequences_into_tree(self):
"""Inserts sequences into Tree using params - test handles tree-insertion"""
# generate temp filename for output
outfname=splitext(get_tmp_filename('/tmp/'))[0]
# create starting tree
outtreefname=outfname+'.tre'
outtree=open(outtreefname,'w')
outtree.write(REF_TREE)
outtree.close()
# set params for tree-insertion
params={}
params["-w"]="/tmp/"
params["-n"] = get_tmp_filename().split("/")[-1]
params["-f"] = 'v'
#params["-G"] = '0.25'
params["-t"] = outtreefname
params["-m"] = 'GTRGAMMA'
aln_ref_query=get_align_for_phylip(StringIO(PHYLIP_FILE_DNA_REF_QUERY))
aln = Alignment(aln_ref_query)
seqs, align_map = aln.toPhylip()
tree = insert_sequences_into_tree(seqs, DNA, params=params,
write_log=False)
for node in tree.tips():
removed_query_str=re.sub('QUERY___','',str(node.Name))
new_node_name=re.sub('___\d+','',str(removed_query_str))
if new_node_name in align_map:
node.Name = align_map[new_node_name]
self.assertTrue(isinstance(tree, PhyloNode))
self.assertEqual(tree.getNewick(with_distances=True),RESULT_TREE)
self.assertEqual(len(tree.tips()), 7)
self.assertRaises(NotImplementedError, build_tree_from_alignment, \
self.align1, RNA, True)
remove(outtreefname)