def read_labelled_supertree(self):
d = os.path.join(self.top_output_dir, 'labelled_supertree')
p = 'labelled_supertree_out_degree_distribution.txt'
lsodd = os.path.join(d, p)
subprocess.call(['make', lsodd])
subprocess.call(['make', os.path.join(d, 'labelled_supertree_ottnames.tre')])
assert(os.path.exists(lsodd))
blob = Extensible()
blob.unprune_stats = read_as_json(os.path.join(d, 'input_output_stats.json'))
blob.non_monophyletic_taxa = read_as_json(os.path.join(d, 'broken_taxa.json'))
if blob.non_monophyletic_taxa['non_monophyletic_taxa'] is None:
blob.non_monophyletic_taxa['non_monophyletic_taxa'] = {}
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_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 perform_separation(taxalotl_config, part_name, id_list, sep_fn):
ott_res = taxalotl_config.get_terminalized_res_by_id(
"ott", 'enforce-new-separators')
if not ott_res.has_been_partitioned():
partition_resources(taxalotl_config, ["ott"], PREORDER_PART_LIST)
sep_mapping_fp = os.path.join(ott_res.partitioned_filepath, SEP_MAPPING)
if not os.path.isfile(sep_mapping_fp):
cache_separator_names(taxalotl_config)
top_dir = get_part_dir_from_part_name(ott_res, part_name)
active_sep_fn = os.path.join(top_dir, sep_fn)
try:
active_seps = return_sep_obj_copy_with_ott_fields(
read_as_json(active_sep_fn))
print(active_seps)
except:
raise ValueError('{} does not exist'.format(part_name, active_sep_fn))
if id_list:
resource_ids = id_list
else:
resource_ids = get_taxonomies_for_dir(top_dir)
for rid in resource_ids:
rw = taxalotl_config.get_resource_by_id(rid)
print(rid, rw)
perform_dynamic_separation(ott_res,
res=rw,
part_key=part_name,
separation_by_ott=active_seps)
def get_separator_dict(self):
from taxalotl.commands import SEP_MAPPING, cache_separator_names
from peyotl import read_as_json
fn = os.path.join(self.partitioned_dir, SEP_MAPPING)
if not os.path.exists(fn):
cache_separator_names(self)
return read_as_json(fn)
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_cleaned_ott(self):
blob = Extensible()
d = os.path.join(self.top_output_dir, 'cleaned_ott')
o = read_as_json(os.path.join(d, 'cleaned_ott.json'))
for k, v in o.items():
setattr(blob, k, v)
if k == 'flags_to_prune':
v.sort()
blob.root_ott_id = self.config.root_ott_id
return blob
def read_labelled_supertree(self):
d = os.path.join(self.top_output_dir, 'labelled_supertree')
p = 'labelled_supertree_out_degree_distribution.txt'
lsodd = os.path.join(d, p)
subprocess.call(['make', lsodd])
subprocess.call(
['make',
os.path.join(d, 'labelled_supertree_ottnames.tre')])
assert (os.path.exists(lsodd))
blob = Extensible()
blob.unprune_stats = read_as_json(
os.path.join(d, 'input_output_stats.json'))
blob.non_monophyletic_taxa = read_as_json(
os.path.join(d, 'broken_taxa.json'))
if blob.non_monophyletic_taxa['non_monophyletic_taxa'] is None:
blob.non_monophyletic_taxa['non_monophyletic_taxa'] = {}
blob.non_monophyletic_taxa = add_taxonomy_metadata(
blob.non_monophyletic_taxa)
return blob
def read_cleaned_ott(self):
blob = Extensible()
d = os.path.join(self.top_output_dir, 'cleaned_ott')
o = read_as_json(os.path.join(d, 'cleaned_ott.json'))
for k, v in o.items():
setattr(blob, k, v)
if k == 'flags_to_prune':
v.sort()
blob.root_ott_id = self.config.root_ott_id
return blob
def read_assessments(self):
d = os.path.join(self.top_output_dir, 'assessments')
blob = Extensible()
blob.assessments = read_as_json(os.path.join(d, 'summary.json'))
blob.categories_of_checks = list(blob.assessments.keys())
blob.categories_of_checks.sort()
blob.categories_of_checks_with_errors = []
for k, v in blob.assessments.items():
if v['result'] != 'OK':
blob.categories_of_checks_with_errors.append(k)
blob.categories_of_checks_with_errors.sort()
return blob
def read_assessments(self):
d = os.path.join(self.top_output_dir, 'assessments')
blob = Extensible()
blob.assessments = read_as_json(os.path.join(d, 'summary.json'))
blob.categories_of_checks = list(blob.assessments.keys())
blob.categories_of_checks.sort()
blob.categories_of_checks_with_errors = []
for k, v in blob.assessments.items():
if v['result'] != 'OK':
blob.categories_of_checks_with_errors.append(k)
blob.categories_of_checks_with_errors.sort()
return blob
def _read_json_and_coerce_to_otttaxon(tax_dir, misc_tax_dir, fn):
r = {}
for td in [tax_dir, misc_tax_dir]:
rf = os.path.join(td, fn)
if os.path.exists(rf):
rd = read_as_json(rf)
for k, v in rd.items():
try:
k = int(k)
except:
pass
r[k] = Taxon(d=v)
return r
def get_auto_gen_part_mapper(res):
fp = os.path.join(res.partitioned_filepath, GEN_MAPPING_FILENAME)
if not os.path.isfile(fp):
m = 'Mapping file not found at "{}"\nRun the build-partitions-maps command.'
raise RuntimeError(m.format(fp))
master_mapping = read_as_json(fp)
a_list = list(res.alias_list)
base_res = res.base_resource
if base_res:
a_list.extend(base_res.alias_list)
poss_ids = [res.id] + a_list + [res.base_id]
for k in poss_ids:
if k in master_mapping:
return master_mapping[k]
m = 'No entry for ids {} found in "{}".'
raise RuntimeError(m.format(', '.join(poss_ids), fp))
parser = argparse.ArgumentParser(
prog=SCRIPT_NAME,
description=
'Simple tool to combine the logs from pruning via flags and pruning via higher-level taxa that have become tips'
)
parser.add_argument('flag_pruned_json', nargs=1, metavar='F', type=str)
parser.add_argument('higher_taxon_pruned_json',
metavar='H',
nargs=1,
type=str)
parser.add_argument('combined_json', nargs=1, metavar='O', type=str)
args = parser.parse_args()
fj_fn = args.flag_pruned_json[0]
htj_fn = args.higher_taxon_pruned_json[0]
out_fn = args.combined_json[0]
blob = read_as_json(fj_fn)
higher_taxon_blob = read_as_json(htj_fn)
if higher_taxon_blob:
p = blob['pruned']
httk = 'higher-taxon-tip'
intk = 'empty-after-higher-taxon-tip-prune'
high_tax_tip_pruned = higher_taxon_blob.get(httk, {})
internal_high_tax_tip_pruned = higher_taxon_blob.get(intk, {})
p[httk] = high_tax_tip_pruned
p[intk] = internal_high_tax_tip_pruned
n_ht_in_pruned = len(internal_high_tax_tip_pruned)
n_ht_pruned = len(high_tax_tip_pruned)
blob['num_non_leaf_nodes'] -= n_ht_in_pruned
blob['num_pruned_anc_nodes'] += n_ht_in_pruned
blob['num_tips'] -= n_ht_pruned
blob['num_nodes'] -= (n_ht_pruned + n_ht_in_pruned)
final_tree = os.path.join(top_dir, 'labelled_supertree', 'labelled_supertree.tre')
# Check that we have the same # of leaves in the cleaned_ott and the final tree
#
tax_dd_file = os.path.join(assessments_dir, 'taxonomy_degree_distribution.txt')
supertree_dd_file = os.path.join(assessments_dir, 'supertree_degree_distribution.txt')
tdd = parse_degree_dist(tax_dd_file)
sdd = parse_degree_dist(supertree_dd_file)
if tdd[0] != sdd[0]:
err('The number of leaves differed between the taxonomy and supertree')
nt = {'result':'ERROR', 'data':[tdd[0][1], sdd[0][1]]}
else:
nt = {'result':'OK', 'data': tdd[0][1]}
nt['description'] = 'Check that the cleaned version of the taxonomy and the supertree have the same number of leaves'
summary['num_tips'] = nt
annot_file = os.path.join(top_dir, 'annotated_supertree', 'annotations.json')
annotations = read_as_json(annot_file)
nodes_annotations = annotations['nodes']
# Check that otc-taxonomy-parser and otc-unprune-solution-and-name-unnamed-nodes
# agree on the number of taxa that were lost
#
if False:
ltb = {'result': 'Skipped test - have not updated tests to deal with 2 layers of taxon filtering', 'data': []}
btb = dict(ltb)
ub = dict(ltb)
else:
lt_file = os.path.join(assessments_dir, 'lost_taxa.txt')
lt_name = 'otc-taxonomy-parser lost-taxon'
lt_pair = [lt_file, lt_name]
lt_set = parse_otc_taxonomy_parser_lost_taxa(lt_file)
bt_file = os.path.join(top_dir, 'labelled_supertree', 'broken_taxa.json')
bt_name = 'otc-unprune-solution-and-name-unnamed-nodes broken_taxa.json'
import sys
if __name__ == '__main__':
import argparse
import os
bin_dir, SCRIPT_NAME = os.path.split(__file__)
propinquity_dir = os.path.dirname(bin_dir)
parser = argparse.ArgumentParser(prog=SCRIPT_NAME, description='Simple tool to combine the logs from pruning via flags and pruning via higher-level taxa that have become tips')
parser.add_argument('flag_pruned_json', nargs=1, metavar='F', type=str)
parser.add_argument('higher_taxon_pruned_json', metavar='H', nargs=1, type=str)
parser.add_argument('combined_json', nargs=1, metavar='O', type=str)
args = parser.parse_args()
fj_fn = args.flag_pruned_json[0]
htj_fn = args.higher_taxon_pruned_json[0]
out_fn = args.combined_json[0]
blob = read_as_json(fj_fn)
higher_taxon_blob = read_as_json(htj_fn)
if higher_taxon_blob:
p = blob['pruned']
httk = 'higher-taxon-tip'
intk = 'empty-after-higher-taxon-tip-prune'
high_tax_tip_pruned = higher_taxon_blob.get(httk, {})
internal_high_tax_tip_pruned = higher_taxon_blob.get(intk, {})
p[httk] = high_tax_tip_pruned
p[intk] = internal_high_tax_tip_pruned
n_ht_in_pruned = len(internal_high_tax_tip_pruned)
n_ht_pruned = len(high_tax_tip_pruned)
blob['num_non_leaf_nodes'] -= n_ht_in_pruned
blob['num_pruned_anc_nodes'] += n_ht_in_pruned
blob['num_tips'] -= n_ht_pruned
blob['num_nodes'] -= (n_ht_pruned + n_ht_in_pruned)
default=None,
type=int,
required=False,
help='Optional taxonomy root argument.')
parser.add_argument('--input-files-list',
default=None,
type=str,
required=False,
help='A list of input NexSON filenames.')
args = parser.parse_args(sys.argv[1:])
ott_dir, out_dir, root = args.ott_dir, args.out_dir, args.root
to_prune_for_reasons = {}
nonflagged_json_fn = args.ott_prune_nonflagged_json
if nonflagged_json_fn is not None:
try:
nonflagged_blob = read_as_json(nonflagged_json_fn)
except:
nonflagged_blob = None
if nonflagged_blob:
for reason, id_list in nonflagged_blob.items():
for ott_id in id_list:
to_prune_for_reasons[ott_id] = reason
flags_str = args.ott_prune_flags
try:
assert os.path.isdir(args.ott_dir)
except:
error('Expecting ott-dir argument to be a directory. Got "{}"'.format(args.ott_dir))
sys.exit(1)
if args.nexson:
inp_files = list(args.nexson)
else:
def main():
import argparse
description = "The main CLI for taxalotl"
p = argparse.ArgumentParser(description=description)
p.add_argument("--config",
type=str,
help="the taxalotl.conf filepath (optional)")
p.add_argument(
"--show-completions",
action="store_true",
default=False,
help="print the list of options for the next word in the command line")
p.set_defaults(which="all")
subp = p.add_subparsers(help="command help")
# ANALYZE UPDATE
analyze_update_p = subp.add_parser(
'analyze-update',
help="calculates a diff between the last version of a "
"taxonomy used and the latest version downloaded.")
analyze_update_p.add_argument('resources',
nargs=2,
help="IDs of the resources to analyzed.")
_add_level_arg(analyze_update_p)
analyze_update_p.set_defaults(which="analyze-update")
# PULL OTifacts
pull_otifacts_p = subp.add_parser(
'pull-otifacts',
help="refresh list of taxonomic artifacts from OTifacts repo")
pull_otifacts_p.set_defaults(which="pull-otifacts")
# STATUS
status_p = subp.add_parser(
'status', help="report the status of a resource (or all resources)")
status_p.add_argument('resources',
nargs="*",
help="IDs of the resources to report status on")
status_p.add_argument("-i",
"--ids-only",
action='store_true',
default=False,
help="just list the IDs")
status_p.add_argument("--by-status",
action='store_true',
default=False,
help="group the report by status")
status_p.add_argument(
"--terminal",
action='store_true',
default=False,
help="Report only on the terminalized resource of each type.")
status_p.set_defaults(which="status")
# CACHE-separator-names
compare_tax_p = subp.add_parser(
'compare-taxonomies', help="compare taxonomies for a separated dir")
_add_level_arg(compare_tax_p)
compare_tax_p.set_defaults(which="compare-taxonomies")
# CACHE-separator-names
cache_p = subp.add_parser(
'cache-separator-names',
help="Accumulate a list of separator names for tab-completion")
cache_p.set_defaults(which="cache-separator-names")
# DOWNLOAD
download_p = subp.add_parser(
'download', help="download an artifact to your local filesystem")
download_p.add_argument('resources',
nargs="+",
help="IDs of the resources to download")
download_p.set_defaults(which="download")
# UNPACK
unpack_p = subp.add_parser(
'unpack', help="unpack an resource (downloads if necessary)")
unpack_p.add_argument('resources',
nargs="+",
help="IDs of the resources to unpack")
unpack_p.set_defaults(which="unpack")
# NORMALIZE
normalize_p = subp.add_parser(
'normalize', help="converts to the OTT format (unpacks if necessary)")
normalize_p.add_argument('resources',
nargs="+",
help="IDs of the resources to normalize")
normalize_p.set_defaults(which="normalize")
# PARTITION
partition_p = subp.add_parser('partition',
help="Breaks the resource taxon")
partition_p.add_argument('resources',
nargs="+",
help="IDs of the resources to partitition")
_add_level_arg(partition_p)
partition_p.set_defaults(which="partition")
# INFO
info_p = subp.add_parser('info', help="Report statistics about a resource")
info_p.add_argument('resources', nargs="+", help="IDs of the resources")
_add_level_arg(info_p)
info_p.set_defaults(which="info")
# DIAGNOSE-NEW-SEPARATORS
diag_sep_p = subp.add_parser(
'diagnose-new-separators',
help="Uses the last OTT build to find taxa IDs that "
"feature are common to the relevant inputs")
_add_level_arg(diag_sep_p)
diag_sep_p.set_defaults(which="diagnose-new-separators")
# ENFORCE-NEW-SEPARATORS
enf_sep_p = subp.add_parser(
'enforce-new-separators',
help="Uses the __sep__.json files created by "
"diagnose-new-separators to partition by unproblematic "
"taxa")
enf_sep_p.add_argument('resources',
nargs="*",
help="IDs of the resources to separate")
_add_level_arg(enf_sep_p)
enf_sep_p.set_defaults(which="enforce-new-separators")
# Align
align_p = subp.add_parser(
'align',
help=
"Attempts to align a new (parititioned) resource to the latest OTT for a level"
)
align_p.add_argument('resources',
nargs="*",
help="IDs of the resources to separate")
_add_level_arg(align_p)
align_p.set_defaults(which="align")
# ACCUMULATE-SEPARATED-DESCENDANTS
accum_sep_des_p = subp.add_parser(
'accumulate-separated-descendants',
help=
"Should be run after enforce-separators and before compare-taxonomies")
accum_sep_des_p.add_argument('resources',
nargs="*",
help="IDs of the resources")
accum_sep_des_p.set_defaults(which="accumulate-separated-descendants")
# BUILD-PARTITION-MAPS
build_partition_maps_p = subp.add_parser(
'build-partition-maps',
help="Uses the last OTT build to find the "
"ID mappings needed to "
"partition the inputs taxonomies.")
build_partition_maps_p.set_defaults(which="build-partition-maps")
# CLEAN-PARTITION
clean_p = subp.add_parser(
'clean-partition',
help=
"remove the results the partition+enforce-new-separator for a resource."
)
clean_p.add_argument('resources',
nargs="*",
help="IDs of the resources to clean")
clean_p.set_defaults(which='clean-partition')
# CLEAN-PARTITION
clean_s_p = subp.add_parser(
'clean-separation',
help="remove the results the diagnose-new-separator for a resource.")
_add_level_arg(clean_s_p)
clean_s_p.set_defaults(which='clean-separation')
# Handle --show-completions differently from the others, because
# argparse does not help us out here... at all
if "--show-completions" in sys.argv:
a = sys.argv[1:]
univ = frozenset([
'--config',
])
sel_cmd = None
num_cmds = 0
for c in all_cmds:
if c in a:
if sel_cmd is None:
sel_cmd = c
num_cmds += 1
comp_list = []
if sel_cmd is None:
comp_list = []
for u in univ:
found = False
for arg in a:
if arg.startswith(u):
found = True
break
if not found:
comp_list.append(u)
comp_list.extend(all_cmds)
else:
if sel_cmd in res_dep_cmds \
or sel_cmd in ['compare-taxonomies'] \
or sel_cmd in ver_inp_res_dep_cmds:
# From Ned Batchelder's answer on http://stackoverflow.com/a/14728477
class ArgumentParserError(Exception):
pass
# noinspection PyClassHasNoInit
class ThrowingArgumentParser(argparse.ArgumentParser):
def error(self, message):
raise ArgumentParserError(message)
fake_parser = ThrowingArgumentParser()
fake_parser.add_argument("--config", type=str)
fake_parser.add_argument('blah', nargs="*")
comp_list = []
taxalotl_config = None
try:
fa = fake_parser.parse_known_args()[0]
config = fa.config
taxalotl_config = TaxalotlConfig(filepath=config)
if sel_cmd in res_dep_cmds:
comp_list = list(
taxalotl_config.resources_mgr.resources.keys())
elif sel_cmd in ver_inp_res_dep_cmds:
comp_list = list(taxalotl_config.resources_mgr.
abstract_input_resource_types())
except Exception as _excep:
_LOG.warn('Exception: {}'.format(_excep))
pass
if sel_cmd == 'status':
if '-i' not in a and '--ids-only' not in a:
comp_list.extend(["-i", "--ids-only"])
for x in ['--by-status', '--terminal']:
if x not in a:
comp_list.extend([x])
elif sel_cmd == 'partition':
# sys.stderr.write(str(a))
if '--level' == a[-1] or (len(a) > 1
and '--level' == a[-2]):
comp_list = list(NONTERMINAL_PART_NAMES)
elif '--level' not in a:
comp_list.extend(['--level'])
elif sel_cmd in ('diagnose-new-separators',
'enforce-new-separators'):
# sys.stderr.write(str(a))
if '--level' == a[-1] or (len(a) > 1
and '--level' == a[-2]):
comp_list = list(TERMINAL_PART_NAMES)
elif '--level' not in a:
comp_list.extend(['--level'])
elif sel_cmd in ['compare-taxonomies']:
rw = taxalotl_config.get_terminalized_res_by_id("ott", '')
outfn = os.path.join(rw.partitioned_filepath, SEP_NAMES)
if os.path.exists(outfn):
comp_list.extend(read_as_json(outfn))
sys.stdout.write('{}\n'.format(' '.join(comp_list)))
else:
rc = main_post_parse(p.parse_args())
sys.exit(rc)
default=None,
type=int,
required=False,
help='Optional taxonomy root argument.')
parser.add_argument('--input-files-list',
default=None,
type=str,
required=False,
help='A list of input NexSON filenames.')
args = parser.parse_args(sys.argv[1:])
ott_dir, out_dir, root = args.ott_dir, args.out_dir, args.root
to_prune_for_reasons = {}
nonflagged_json_fn = args.ott_prune_nonflagged_json
if nonflagged_json_fn is not None:
try:
nonflagged_blob = read_as_json(nonflagged_json_fn)
except:
nonflagged_blob = None
if nonflagged_blob:
for reason, id_list in nonflagged_blob.items():
for ott_id in id_list:
to_prune_for_reasons[ott_id] = reason
flags_str = args.ott_prune_flags
try:
assert os.path.isdir(args.ott_dir)
except:
error('Expecting ott-dir argument to be a directory. Got "{}"'.format(
args.ott_dir))
sys.exit(1)
if args.nexson:
inp_files = list(args.nexson)
def get_primary_partition_map(self):
return read_as_json(
os.path.join(self.normalized_filedir, GEN_MAPPING_FILENAME))
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
#!/usr/bin/env python
from peyotl import read_as_json
import codecs
import json
import sys
try:
subproblem_ids_file, in_annotations_file, out_annotations_file = sys.argv[1:]
except:
sys.exit('Expecting 3 arguments:\n subproblem_ids_file, in_annotations_file, out_annotations_file')
import os
bin_dir = os.path.abspath(os.path.dirname(sys.argv[0]))
sys.path.append(os.path.join(bin_dir))
from document_outputs import stripped_nonempty_lines
subproblems = []
for s in stripped_nonempty_lines(subproblem_ids_file):
assert s.endswith('.tre')
subproblems.append(s[:-4])
jsonblob = read_as_json(in_annotations_file)
nodes_dict = jsonblob['nodes']
for ott_id in subproblems:
d = nodes_dict.setdefault(ott_id, {})
d['was_constrained'] = True
d['was_uncontested'] = True
with codecs.open(out_annotations_file, 'w', encoding='utf-8') as out_stream:
json.dump(jsonblob, out_stream, indent=2, sort_keys=True, separators=(',', ': '))
#!/usr/bin/env python
from peyotl import concatenate_collections, read_as_json, write_as_json
if __name__ == '__main__':
import argparse
import sys
import os
description = 'Takes a list of collections and writes a collection that is a concatenation of their decisions'
parser = argparse.ArgumentParser(prog='collection_export.py', description=description)
parser.add_argument('--output',
type=str,
required=True,
help='output filepath for collection json')
parser.add_argument('collection',
default=None,
type=str,
nargs="*",
help='filepath for the collections JSON')
args = parser.parse_args(sys.argv[1:])
inp = [read_as_json(i) for i in args.collection]
out = concatenate_collections(inp)
write_as_json(out, args.output)
nt = {'result':'ERROR', 'data':[tdd[0][1], sdd[0][1]]}
else:
nt = {'result':'OK', 'data': tdd[0][1]}
nt['description'] = 'Check that the cleaned version of the taxonomy and the supertree have the same number of leaves'
summary['num_tips'] = nt
# Check that otc-taxonomy-parser and otc-unprune-solution-and-name-unnamed-nodes
# agree on the number of taxa that were lost
#
lt_file = os.path.join(assessments_dir, 'lost_taxa.txt')
lt_name = 'otc-taxonomy-parser lost-taxon'
lt_pair = [lt_file, lt_name]
lt_set = parse_otc_taxonomy_parser_lost_taxa(lt_file)
bt_file = os.path.join(top_dir, 'labelled_supertree', 'broken_taxa.json')
bt_name = 'otc-unprune-solution-and-name-unnamed-nodes broken_taxa.json'
bt_pair = [bt_file, bt_name]
bt_dict = read_as_json(bt_file)['non_monophyletic_taxa']
if not bt_dict:
bt_dict = {}
cleaned_ott_json_pruned = read_as_json(cleaned_taxonomy_json).get('pruned', {})
# pruned because they became empty
httip_key = 'higher-taxon-tip'
int_key = 'empty-after-higher-taxon-tip-prune'
htpruned_ids = set()
for key in [httip_key, int_key]:
pl = set(cleaned_ott_json_pruned.get(key, []))
htpruned_ids.update(pl)
lte = {}
for ott_id in lt_set:
ott_id_str = 'ott{}'.format(ott_id)
if (ott_id_str not in bt_dict) and (ott_id not in htpruned_ids):
import codecs
import json
import sys
try:
subproblem_ids_file, in_annotations_file, out_annotations_file = sys.argv[
1:]
except:
sys.exit(
'Expecting 3 arguments:\n subproblem_ids_file, in_annotations_file, out_annotations_file'
)
import os
bin_dir = os.path.abspath(os.path.dirname(sys.argv[0]))
sys.path.append(os.path.join(bin_dir))
from document_outputs import stripped_nonempty_lines
subproblems = []
for s in stripped_nonempty_lines(subproblem_ids_file):
assert s.endswith('.tre')
subproblems.append(s[:-4])
jsonblob = read_as_json(in_annotations_file)
nodes_dict = jsonblob['nodes']
for ott_id in subproblems:
d = nodes_dict.setdefault(ott_id, {})
d['was_constrained'] = True
d['was_uncontested'] = True
with codecs.open(out_annotations_file, 'w', encoding='utf-8') as out_stream:
json.dump(jsonblob,
out_stream,
indent=2,
sort_keys=True,
separators=(',', ': '))
