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 test_build_tree_from_alignment_using_params(self):
"""Builds a tree from a json file"""
# define working directory for output
outdir='/tmp/'
# set params
params={}
params["tog"] = None
# build tree
tree = build_tree_from_json_using_params(self.json_fname,
output_dir=outdir,
params=params)
self.assertEqual(tree.getNewick(),
DndParser(TREE_RESULT, constructor=PhyloNode).getNewick())
def test_build_tree_from_alignment_using_params(self):
"""Builds a tree from a json file"""
# define working directory for output
outdir = '/tmp/'
# set params
params = {}
params["tog"] = None
# build tree
tree = build_tree_from_json_using_params(self.json_fname,
output_dir=outdir,
params=params)
self.assertEqual(
tree.getNewick(),
DndParser(TREE_RESULT, constructor=PhyloNode).getNewick())
