def read_exemplified_phylo(self):
d = os.path.join(self.top_output_dir, 'exemplified_phylo')
x = read_as_json(os.path.join(d, 'exemplified_log.json'))
tx = x['taxa_exemplified']
if not tx:
tx = {}
by_source_tree = {}
for ott_id, exdict in tx.items():
tm = exdict['trees_modified']
for tree in tm:
key = '.'.join(tree.split('.')[:-1])
by_source_tree.setdefault(key, []).append(ott_id)
for v in by_source_tree.values():
v.sort()
ptdd = os.path.join(d, 'pruned_taxonomy_degree_distribution.txt')
subprocess.call(['make', ptdd])
assert (os.path.exists(ptdd))
ddlines = [
i.split() for i in stripped_nonempty_lines(ptdd)
if i.split()[0] == '0'
]
assert (len(ddlines) == 1)
leaf_line = ddlines[0] # should b
assert (len(leaf_line) == 2)
blob = Extensible()
blob.num_leaves_in_exemplified_taxonomy = int(leaf_line[1])
blob.taxa_exemplified = tx
blob.source_tree_to_ott_id_exemplified_list = by_source_tree
f = os.path.join(d, 'nonempty_trees.txt')
blob.nonempty_tree_filenames = stripped_nonempty_lines(f)
blob.nonempty_trees = [
propinquity_fn_to_study_tree(i)
for i in blob.nonempty_tree_filenames
]
return blob
def read_phylo_input(self):
blob = Extensible()
blob.directory = os.path.join(self.top_output_dir, 'phylo_input')
blob.study_tree_pair_file = os.path.join(blob.directory, 'study_tree_pairs.txt')
x = stripped_nonempty_lines(blob.study_tree_pair_file)
blob.study_id_tree_id_pairs = [propinquity_fn_to_study_tree(i, strip_extension=False) for i in x]
return blob
def read_exemplified_phylo(self):
d = os.path.join(self.top_output_dir, 'exemplified_phylo')
x = read_as_json(os.path.join(d, 'exemplified_log.json'))
tx = x['taxa_exemplified']
if not tx:
tx = {}
by_source_tree = {}
for ott_id, exdict in tx.items():
tm = exdict['trees_modified']
for tree in tm:
key = '.'.join(tree.split('.')[:-1])
by_source_tree.setdefault(key, []).append(ott_id)
for v in by_source_tree.values():
v.sort()
ptdd = os.path.join(d, 'pruned_taxonomy_degree_distribution.txt')
subprocess.call(['make', ptdd])
assert(os.path.exists(ptdd))
ddlines = [i.split() for i in stripped_nonempty_lines(ptdd) if i.split()[0] == '0']
assert(len(ddlines) == 1)
leaf_line = ddlines[0] # should b
assert(len(leaf_line) == 2)
blob = Extensible()
blob.num_leaves_in_exemplified_taxonomy = int(leaf_line[1])
blob.taxa_exemplified = tx
blob.source_tree_to_ott_id_exemplified_list = by_source_tree
f = os.path.join(d, 'nonempty_trees.txt')
blob.nonempty_tree_filenames = stripped_nonempty_lines(f)
blob.nonempty_trees = [propinquity_fn_to_study_tree(i) for i in blob.nonempty_tree_filenames]
return blob
def read_subproblems(self):
d = os.path.join(self.top_output_dir, 'subproblems')
blob = Extensible()
conf_tax_json_fp = os.path.join(d, 'contesting-trees.json')
conf_tax_info = read_as_json(conf_tax_json_fp)
if not conf_tax_info:
conf_tax_info = {}
externalized_conf_tax_info = {}
for ott_id, tree2node_info_list in conf_tax_info.items():
tr_ob_li = []
if ott_id.startswith('ott'):
ott_id = ott_id[3:]
externalized_conf_tax_info[ott_id] = tr_ob_li
for study_tree_fn, node_info_list in tree2node_info_list.items():
study_id, tree_id = propinquity_fn_to_study_tree(study_tree_fn)
cf_nl = []
tre_obj = {'study_id': study_id,
'tree_id': tree_id,
'tree_filename': study_tree_fn,
'conflicting_nodes': cf_nl}
tr_ob_li.append(tre_obj)
if len(node_info_list) < 2:
raise RuntimeError('read_subproblems < 2 node info elements for taxon ID = {}'.format(ott_id))
for node_info in node_info_list:
rcfn = node_info['children_from_taxon']
cfn = [node_label2obj(i) for i in rcfn]
el = {'parent': node_label2obj(node_info['parent']),
'children_from_taxon': cfn
}
cf_nl.append(el)
blob.contested_taxa = externalized_conf_tax_info
blob.tree_files = stripped_nonempty_lines(os.path.join(d, 'subproblem-ids.txt'))
id2num_leaves = {}
for el in self.subproblem_solutions.subproblem_num_leaves_num_internal_nodes:
id2num_leaves[el[0]] = el[1]
by_num_phylo = []
by_input = {}
for s in blob.tree_files:
assert s.endswith('.tre')
pref = s[:-4]
assert pref.startswith('ott')
tree_name_file = os.path.join(d, pref + '-tree-names.txt')
phylo_inputs = []
for i in stripped_nonempty_lines(tree_name_file):
x = i[:-4] if i.endswith('.tre') else i
phylo_inputs.append(i)
if x != 'TAXONOMY':
by_input.setdefault(x, []).append(pref)
npi = len(phylo_inputs)
by_num_phylo.append((npi, int(pref[3:]), s, phylo_inputs))
by_num_phylo.sort(reverse=True)
blob.sorted_by_num_phylo_inputs = [[i[2], i[3], id2num_leaves[i[2]]] for i in by_num_phylo]
by_input = [(len(v), k, v) for k, v in by_input.items()]
by_input.sort(reverse=True)
blob.input_and_subproblems_sorted = [[i[1], i[2]] for i in by_input]
return blob
def read_phylo_input(self):
blob = Extensible()
blob.directory = os.path.join(self.top_output_dir, 'phylo_input')
blob.study_tree_pair_file = os.path.join(blob.directory,
'study_tree_pairs.txt')
x = stripped_nonempty_lines(blob.study_tree_pair_file)
blob.study_id_tree_id_pairs = [
propinquity_fn_to_study_tree(i, strip_extension=False) for i in x
]
return blob
def read_subproblems(self):
d = os.path.join(self.top_output_dir, 'subproblems')
blob = Extensible()
conf_tax_json_fp = os.path.join(d, 'contesting-trees.json')
conf_tax_info = read_as_json(conf_tax_json_fp)
if not conf_tax_info:
conf_tax_info = {}
externalized_conf_tax_info = {}
for ott_id, tree2node_info_list in conf_tax_info.items():
tr_ob_li = []
if ott_id.startswith('ott'):
ott_id = ott_id[3:]
externalized_conf_tax_info[ott_id] = tr_ob_li
for study_tree_fn, node_info_list in tree2node_info_list.items():
study_id, tree_id = propinquity_fn_to_study_tree(study_tree_fn)
cf_nl = []
tre_obj = {
'study_id': study_id,
'tree_id': tree_id,
'tree_filename': study_tree_fn,
'conflicting_nodes': cf_nl
}
tr_ob_li.append(tre_obj)
if len(node_info_list) < 2:
raise RuntimeError(
'read_subproblems < 2 node info elements for taxon ID = {}'
.format(ott_id))
for node_info in node_info_list:
rcfn = node_info['children_from_taxon']
cfn = [node_label2obj(i) for i in rcfn]
el = {
'parent': node_label2obj(node_info['parent']),
'children_from_taxon': cfn
}
cf_nl.append(el)
blob.contested_taxa = externalized_conf_tax_info
blob.tree_files = stripped_nonempty_lines(
os.path.join(d, 'subproblem-ids.txt'))
id2num_leaves = {}
for el in self.subproblem_solutions.subproblem_num_leaves_num_internal_nodes:
id2num_leaves[el[0]] = el[1]
by_num_phylo = []
by_input = {}
for s in blob.tree_files:
assert s.endswith('.tre')
pref = s[:-4]
assert pref.startswith('ott')
tree_name_file = os.path.join(d, pref + '-tree-names.txt')
phylo_inputs = []
for i in stripped_nonempty_lines(tree_name_file):
x = i[:-4] if i.endswith('.tre') else i
phylo_inputs.append(i)
if x != 'TAXONOMY':
by_input.setdefault(x, []).append(pref)
npi = len(phylo_inputs)
by_num_phylo.append((npi, int(pref[3:]), s, phylo_inputs))
by_num_phylo.sort(reverse=True)
blob.sorted_by_num_phylo_inputs = [[i[2], i[3], id2num_leaves[i[2]]]
for i in by_num_phylo]
by_input = [(len(v), k, v) for k, v in by_input.items()]
by_input.sort(reverse=True)
blob.input_and_subproblems_sorted = [[i[1], i[2]] for i in by_input]
return blob
in_dir = args.input_dir
if in_dir:
in_dir = os.path.expanduser(in_dir)
inp_files = [os.path.join(in_dir, i) for i in inp_files]
if flags_str is None:
flags = OTT.TREEMACHINE_SUPPRESS_FLAGS
else:
flags = flags_str.split(',')
ott = OTT(ott_dir=args.ott_dir)
to_prune_fsi_set = ott.convert_flag_string_set_to_union(flags)
for inp in inp_files:
_LOG.debug('{}'.format(inp))
log_obj = {}
inp_fn = os.path.split(inp)[-1]
study_tree = '.'.join(inp_fn.split('.')[:-1]) # strip extension
study_id, tree_id = propinquity_fn_to_study_tree(inp_fn)
nexson_blob = read_as_json(inp)
ntw = NexsonTreeWrapper(nexson_blob, tree_id, log_obj=log_obj)
assert ntw.root_node_id
taxonomy_treefile = os.path.join(args.out_dir, study_tree + '-taxonomy.tre')
try:
ntw.prune_tree_for_supertree(ott=ott,
to_prune_fsi_set=to_prune_fsi_set,
root_ott_id=root,
taxonomy_treefile=taxonomy_treefile,
id_to_other_prune_reason=to_prune_for_reasons)
except EmptyTreeError:
log_obj['EMPTY_TREE'] = True
out_log = os.path.join(args.out_dir, study_tree + '.json')
write_as_json(log_obj, out_log)
newick_fp = os.path.join(args.out_dir, study_tree + '.tre')
#!/usr/bin/env python
"""Takes meta properties for a tree requested"""
from __future__ import absolute_import, division, print_function, unicode_literals
from peyotl.api import PhylesystemAPI
from peyotl.utility import propinquity_fn_to_study_tree
import codecs
import sys
out = codecs.getwriter('utf-8')(sys.stdout)
NON_META = frozenset([u'^ot:rootNodeId',
u'nodeById',
u'edgeBySourceId',
u'^ot:inGroupClade',
u'@xsi:type',
u'^ot:branchLengthTimeUnit',
u'^ot:branchLengthDescription',
u'^ot:tag',
u'^ot:branchLengthMode'])
for arg in sys.argv[1:]:
study_id, tree_id = propinquity_fn_to_study_tree(arg, strip_extension=False)
pa = PhylesystemAPI(get_from='local')
try:
tree = pa.get(study_id, tree_id=tree_id)[tree_id]
print('Tree "{}" in study "{}":'.format(tree_id, study_id))
for k, v in tree.items():
if (v is not None) and (v is not '') and (k not in NON_META):
print(k, v)
except:
sys.stderr.write('WARNING: did not find tree "{}" in study "{}"'.format(tree_id, study_id))
in_dir = args.input_dir
if in_dir:
in_dir = os.path.expanduser(in_dir)
inp_files = [os.path.join(in_dir, i) for i in inp_files]
if flags_str is None:
flags = OTT.TREEMACHINE_SUPPRESS_FLAGS
else:
flags = flags_str.split(',')
ott = OTT(ott_dir=args.ott_dir)
to_prune_fsi_set = ott.convert_flag_string_set_to_union(flags)
for inp in inp_files:
_LOG.debug('{}'.format(inp))
log_obj = {}
inp_fn = os.path.split(inp)[-1]
study_tree = '.'.join(inp_fn.split('.')[:-1]) # strip extension
study_id, tree_id = propinquity_fn_to_study_tree(inp_fn)
nexson_blob = read_as_json(inp)
ntw = NexsonTreeWrapper(nexson_blob, tree_id, log_obj=log_obj)
assert ntw.root_node_id
taxonomy_treefile = os.path.join(args.out_dir,
study_tree + '-taxonomy.tre')
try:
ntw.prune_tree_for_supertree(
ott=ott,
to_prune_fsi_set=to_prune_fsi_set,
root_ott_id=root,
taxonomy_treefile=taxonomy_treefile,
id_to_other_prune_reason=to_prune_for_reasons)
except EmptyTreeError:
log_obj['EMPTY_TREE'] = True
out_log = os.path.join(args.out_dir, study_tree + '.json')