def get_response_content(fs):
headers, sequences = Phylip.decode(fs.phylip.splitlines())
if fs.name not in headers:
raise ValueError('the name was not found')
new_pairs = [(h, s) for h, s in zip(headers, sequences) if h != fs.name]
new_headers, new_sequences = zip(*new_pairs)
return Phylip.encode(new_headers, new_sequences) + '\n'
def get_response_content(fs):
headers, sequences = Phylip.decode(fs.phylip.splitlines())
if fs.name not in headers:
raise ValueError('the name was not found')
new_pairs = [(h, s) for h, s in zip(headers, sequences) if h != fs.name]
new_headers, new_sequences = zip(*new_pairs)
return Phylip.encode(new_headers, new_sequences) + '\n'
def process(fs, raw_lines):
headers, sequences = Phylip.decode(raw_lines)
binary_rows = Carbone.get_binary_rows(sequences)
if fs.hud:
return hud.encode(headers, binary_rows) + '\n'
elif fs.phy:
binary_seqs = [''.join(str(x) for x in row) for row in binary_rows]
return Phylip.encode(headers, binary_seqs) + '\n'
def run_in_tmp(fs, nexus):
"""
@param fs: fieldstorage-like user options
@param nexus: the nexus object that defines the tree and alignment
@return: from_paml
"""
# create the control object
config = Paml.PamlConfig()
config.set_hky()
# create the baseml.ctl control file
ctl_string = config.to_ctl_string()
with open(Paml.baseml_ctl, 'wt') as fout:
print >> fout, ctl_string
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(Paml.baseml_newick, 'wt') as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
s_phylip = Phylip.get_alignment_string_non_interleaved(nexus.alignment)
with open(Paml.baseml_phylip, 'wt') as fout:
print >> fout, s_phylip
# run PAML
args = [Config.baseml_exe_path, Paml.baseml_ctl]
from_paml, to_paml = popen2.popen4(args)
return from_paml
def run_in_tmp(fs, nexus):
"""
@param fs: fieldstorage-like user options
@param nexus: the nexus object that defines the tree and alignment
@return: from_paml
"""
# create the control object
config = Paml.PamlConfig()
config.set_hky()
# create the baseml.ctl control file
ctl_string = config.to_ctl_string()
with open(Paml.baseml_ctl, 'wt') as fout:
print >> fout, ctl_string
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(Paml.baseml_newick, 'wt') as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
s_phylip = Phylip.get_alignment_string_non_interleaved(nexus.alignment)
with open(Paml.baseml_phylip, 'wt') as fout:
print >> fout, s_phylip
# run PAML
args = [Config.baseml_exe_path, Paml.baseml_ctl]
from_paml, to_paml = popen2.popen4(args)
return from_paml
def run_hky(tree, alignment):
"""
@param tree: a tree object
@param alignment: an alignment object
@return: messages from the program but not the results
"""
# create the baseml.ctl control file
config = PamlConfig()
config.set_hky()
config.to_ctl_string()
with open(baseml_ctl, 'wt') as fout:
print >> fout, config.to_ctl_string()
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(baseml_newick, 'wt') as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
phylip_string = Phylip.get_alignment_string_non_interleaved(
nexus.alignment)
with open(baseml_phylip, 'wt') as fout:
print >> fout, phylip_string
# change the current directory to the data directory
with Util.remember_cwd():
os.chdir(Config.data_path)
# run PAML
exe_path = Config.baseml_exe_path
ctl_path = baseml_ctl
#cmd = '%s %s > /dev/null' % (exe_path, ctl_path)
#os.system(cmd)
from_paml, to_paml = popen2.popen4([exe_path, ctl_path])
#p = subprocess.Popen([cmd, arg], stdin=subprocess.PIPE, stdout=subprocess.PIPE, close_fds=True)
# change back to the old directory
return from_paml.read()
def run_hky(tree, alignment):
"""
@param tree: a tree object
@param alignment: an alignment object
@return: messages from the program but not the results
"""
# create the baseml.ctl control file
config = PamlConfig()
config.set_hky()
config.to_ctl_string()
with open(baseml_ctl, "wt") as fout:
print >> fout, config.to_ctl_string()
# create the nexus object that defines the tree and alignment
nexus = Nexus.get_sample_nexus_object()
# create the baseml.newick tree file
with open(baseml_newick, "wt") as fout:
print >> fout, nexus.tree.get_newick_string()
# create the baseml.phylip alignment file
phylip_string = Phylip.get_alignment_string_non_interleaved(nexus.alignment)
with open(baseml_phylip, "wt") as fout:
print >> fout, phylip_string
# change the current directory to the data directory
with Util.remember_cwd():
os.chdir(Config.data_path)
# run PAML
exe_path = Config.baseml_exe_path
ctl_path = baseml_ctl
# cmd = '%s %s > /dev/null' % (exe_path, ctl_path)
# os.system(cmd)
from_paml, to_paml = popen2.popen4([exe_path, ctl_path])
# p = subprocess.Popen([cmd, arg], stdin=subprocess.PIPE, stdout=subprocess.PIPE, close_fds=True)
# change back to the old directory
return from_paml.read()
def get_response_content(fs):
headers, sequences = Phylip.decode(fs.phylip.splitlines())
phylip_columns = zip(*sequences)
counts = [len(set(col)) for col in phylip_columns]
header_low_high = []
k = 0 if fs.from_zero else 1
for i, count in enumerate(counts):
if not (count == 1 and fs.remove):
low = k
high = k + (count - 1)
header_low_high.append((i+(1 if fs.from_one else 0), low, high))
k += count
out = StringIO()
for triple in header_low_high:
print >> out, 'locus%s.phy\t%d-%d' % triple
return out.getvalue()
def get_response_content(fs):
# get the combo info
combo_triples = list(gen_combo_line_triples(fs.combo.splitlines()))
names, lows, highs = zip(*combo_triples)
ranges = zip(lows, highs)
if lows[0] != 1:
raise ValueError('expected the first lower bound to be 1')
for (low, high), (nlow, nhigh) in iterutils.pairwise(ranges):
if high + 1 != nlow:
raise ValueError(
'expected the next lower bound '
'to be one more than the current upper bound')
# get the phylip info
headers, sequences = Phylip.decode(fs.phylip.splitlines())
phylip_columns = zip(*sequences)
counts = [len(set(col)) for col in phylip_columns]
# validate the compatibility between the combo and phylip data
if highs[-1] != len(phylip_columns):
raise ValueError(
'expected the last upper bound to be '
'equal to the number of columns of the phylip alignment')
# get the sum of counts in each combination group
combo_counts = []
for i, (low, high) in enumerate(ranges):
combo_count = 0
# note that low and high are 1-based and inclusive
for j in range(low-1, high):
combo_count += counts[j]
combo_counts.append(combo_count)
# write the new combo log
out = StringIO()
print >> out, 'Loci combined'
print >> out
k = 0
for name, count in zip(names, combo_counts):
low = k + 1
high = k + count
print >> out, '%s\t%d-%d' % (name, low, high)
k += count
return out.getvalue()
def get_response_content(fs):
headers, sequences = Phylip.decode(fs.phylip.splitlines())
new_pairs = sorted(zip(headers, sequences))
new_headers, new_sequences = zip(*new_pairs)
return Phylip.encode(new_headers, new_sequences) + '\n'
def get_response_content(fs):
headers, sequences = Phylip.decode(fs.phylip.splitlines())
new_pairs = sorted(zip(headers, sequences))
new_headers, new_sequences = zip(*new_pairs)
return Phylip.encode(new_headers, new_sequences) + '\n'
def get_response_content(fs):
headers, data_rows = hud.decode(fs.table.splitlines())
sequences = [''.join(str(x) for x in row) for row in data_rows]
return Phylip.encode(headers, sequences)
def get_response_content(fs):
headers, data_rows = hud.decode(fs.table.splitlines())
sequences = [''.join(str(x) for x in row) for row in data_rows]
return Phylip.encode(headers, sequences)
