name), metadata=True)
else:
tree = Tree()
tree.read_from_file('{0}/trees/{1}.nwk'.format(working_dir,
name))
dv_matrix_strip_header = '\n'.join(dv_matrix.split('\n'
)[2:]).rstrip()
labels_strip_header = labels.split('\n')[1].rstrip()
record = TCSeqRec()
record.dv = [(dv_matrix_strip_header, labels_strip_header)]
record.tree = tree
record.name = name
record.headers = labels_strip_header.split()
record.sequences = ['' for _ in record.headers]
record._update()
records.append(record)
collection = SequenceCollection(records=records, get_distances=False,
gtp_path=os.environ['GTP_PATH'])
collection.put_distance_matrices('rf')
T = \
collection.Clustering.run_spectral_rotate(collection.distance_matrices['rf'
])
collection.partitions[T] = Partition(T)
collection.clusters_to_partitions[('rf', 'spectral_rotate', max(T))] = T
collection.concatenate_records()
cluster_recs = collection.get_cluster_records()
number_of_clusters = len(cluster_recs)
for j in range(number_of_clusters):
def simulate_from_record_WAG(
cls,
record,
output_dir,
name='tempsim',
tmpdir='/tmp',
allow_nonsense=False,
split_lengths=None,
gene_names=None,
):
length = record.seqlength
tree = record.tree
directorycheck_and_quit(tmpdir)
gamma = tree.extract_gamma_parameter()
param_dir = '{0}/alf_parameter_dir'.format(tmpdir)
working_dir = '{0}/alf_working_dir'.format(tmpdir)
directorycheck_and_make(param_dir, verbose=False)
directorycheck_and_make(working_dir, verbose=False)
treefile = '{0}/treefile.nwk'.format(tmpdir)
tree.pam2sps('sps2pam').write_to_file(treefile)
directorycheck_and_make(param_dir)
directorycheck_and_make(working_dir)
sim = cls(simulation_name=name, working_directory=working_dir,
outfile_path=param_dir, unit_is_pam=True)
sim.indels()
sim.rate_variation(gamma)
sim.root_genome(number_of_genes=1, min_length=length)
sim.one_word_model('WAG')
sim.custom_tree(treefile)
params = sim.write_parameters()
sim.runALF(params, quiet=True)
tree_newick = tree.newick
alf_newick = \
open('{0}/alf_working_dir/{1}/RealTree.nwk'.format(tmpdir,
name)).read()
replacement_dict = dict(zip(re.findall(r'(\w+)(?=:)',
alf_newick), re.findall(r'(\w+)(?=:)',
tree_newick))) # bug correction
alignment = \
glob.glob('{0}/alf_working_dir/{1}/MSA/*aa.fa'.format(tmpdir,
name))[0]
new_record = TCSeqRec(alignment)
new_record.sequences = [seq[:length] for seq in
new_record.sequences]
new_record._update()
print new_record.seqlength
new_record.headers = [replacement_dict[x[:x.rindex('/')]]
for x in new_record.headers] # bug should be fixed
new_record._update()
new_record.sort_by_name()
if split_lengths and gene_names:
with open('{0}/trees.txt'.format(output_dir), 'a') as trf:
trf.write('{0}\t{1}\n'.format('-'.join(gene_names), tree.newick))
for rec in new_record.split_by_lengths(split_lengths,
gene_names):
rec.write_phylip('{0}/{1}.phy'.format(output_dir,
rec.name))
else:
with open('{0}/trees.txt'.format(output_dir), 'a') as trf:
trf.write('{0}\t{1}\n'.format(new_record.name, tree.newick))
new_record.write_phylip('{0}/{1}.phy'.format(output_dir,
name))
shutil.rmtree(param_dir)
shutil.rmtree(working_dir)
def simulate_from_record_WAG(
cls,
record,
output_dir,
name='tempsim',
tmpdir='/tmp',
allow_nonsense=False,
split_lengths=None,
gene_names=None,
):
length = record.seqlength
tree = record.tree
directorycheck_and_quit(tmpdir)
gamma = tree.extract_gamma_parameter()
param_dir = '{0}/alf_parameter_dir'.format(tmpdir)
working_dir = '{0}/alf_working_dir'.format(tmpdir)
directorycheck_and_make(param_dir, verbose=False)
directorycheck_and_make(working_dir, verbose=False)
treefile = '{0}/treefile.nwk'.format(tmpdir)
tree.pam2sps('sps2pam').write_to_file(treefile)
directorycheck_and_make(param_dir)
directorycheck_and_make(working_dir)
sim = cls(simulation_name=name,
working_directory=working_dir,
outfile_path=param_dir,
unit_is_pam=True)
sim.indels()
sim.rate_variation(gamma)
sim.root_genome(number_of_genes=1, min_length=length)
sim.one_word_model('WAG')
sim.custom_tree(treefile)
params = sim.write_parameters()
sim.runALF(params, quiet=True)
tree_newick = tree.newick
alf_newick = \
open('{0}/alf_working_dir/{1}/RealTree.nwk'.format(tmpdir,
name)).read()
replacement_dict = dict(
zip(re.findall(r'(\w+)(?=:)', alf_newick),
re.findall(r'(\w+)(?=:)', tree_newick))) # bug correction
alignment = \
glob.glob('{0}/alf_working_dir/{1}/MSA/*aa.fa'.format(tmpdir,
name))[0]
new_record = TCSeqRec(alignment)
new_record.sequences = [seq[:length] for seq in new_record.sequences]
new_record._update()
print new_record.seqlength
new_record.headers = [
replacement_dict[x[:x.rindex('/')]] for x in new_record.headers
] # bug should be fixed
new_record._update()
new_record.sort_by_name()
if split_lengths and gene_names:
with open('{0}/trees.txt'.format(output_dir), 'a') as trf:
trf.write('{0}\t{1}\n'.format('-'.join(gene_names),
tree.newick))
for rec in new_record.split_by_lengths(split_lengths, gene_names):
rec.write_phylip('{0}/{1}.phy'.format(output_dir, rec.name))
else:
with open('{0}/trees.txt'.format(output_dir), 'a') as trf:
trf.write('{0}\t{1}\n'.format(new_record.name, tree.newick))
new_record.write_phylip('{0}/{1}.phy'.format(output_dir, name))
shutil.rmtree(param_dir)
shutil.rmtree(working_dir)
