def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage=
'Display taxonomic info (based on the Open Tree Taxonomy) for a taxon ID',
common_args=("ott-id", ))
cli.parser.add_argument(
'--source-id',
default=None,
type=str,
help=
'A source taxonomy id for the taxon of interest, in the form prefix:id, for'
' example ncbi:9443, irmng:11338. '
'Valid prefixes are currently ncbi, gbif, worms, if, and irmng. '
'Either ott_id or source_id must be given, but not both')
cli.parser.add_argument(
'--include-lineage',
action='store_true',
help='Return the lineage of nodes back to the root of the tree')
cli.parser.add_argument(
'--include-children',
action='store_true',
help='Return information about all the children of this taxon')
cli.parser.add_argument(
'--include-terminal-descendants',
action='store_true',
help=
'Return a list of terminal OTT IDs that are descendants of this taxon')
OT, args = cli.parse_cli(arg_list)
kwargs = {
'include_children': args.include_children,
'include_lineage': args.include_lineage,
'include_terminal_descendants': args.include_terminal_descendants,
}
if args.ott_id:
o = args.ott_id if not args.ott_id.startswith(
'ott') else args.ott_id[3:]
try:
ott_id = int(o)
except:
raise RuntimeError(
'Expecting each ott ID to be an integer or a string starting with "ott". '
'Found "{}"\n'.format(args.ott_id))
else:
output = OT.taxon_info(ott_id=ott_id, **kwargs)
elif args.source_id:
if ':' not in args.source_id:
raise RuntimeError(
'Expecting a source ID to be in prefix:ID form. '
'Found "{}"\n'.format(args.source_id))
output = OT.taxon_info(source_id=args.source_id, **kwargs)
else:
raise RuntimeError(
'Expecting either --ott-id or --source-id to be provided\n')
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sp = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sp))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(usage='Look up the OTT IDs for a set of names')
cli.parser.add_argument("names", nargs="+", help="names to match")
cli.parser.add_argument(
"--context-name",
default=None,
help=
'If you know the named Open Tree name searching index, you can supply it here '
'to limit your search to only a subset of the taxonomny.')
cli.parser.add_argument("--do-approximate-matching",
action="store_true",
help='Enables fuzzy matching')
cli.parser.add_argument(
"--include-suppressed",
action="store_true",
help='Return taxa that are normally suppressed from TNRS '
'results. See {}'.format(get_suppressed_taxon_flag_expl_url()))
OT, args = cli.parse_cli(arg_list)
resp = OT.tnrs_match(args.names,
context_name=args.context_name,
do_approximate_matching=args.do_approximate_matching,
include_suppressed=args.include_suppressed)
if list_for_results is not None:
list_for_results.append(resp)
if out is not None:
sf = json.dumps(resp.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sf))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage=
'Look up studies in the "phylesystem" set of phylogenetic studies that are in the Open '
'system')
cli.parser.add_argument("value", help="The value of the property to match")
cli.parser.add_argument("--property",
default=None,
required=True,
help='The name of the field to search through.')
cli.parser.add_argument("--verbose",
action="store_true",
help='include meta-data in response')
cli.parser.add_argument("--exact",
action="store_true",
help='disables fuzzy matching')
OT, args = cli.parse_cli(arg_list)
output = OT.find_studies(args.value,
search_property=args.property,
verbose=args.verbose,
exact=args.exact)
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sf = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sf))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage='Display node info for the synthetic tree node(s) requested',
common_args=("ott-ids", "node-ids"))
cli.parser.add_argument(
'--include-lineage',
action='store_true',
help='Return the lineage of nodes back to the root of the tree')
OT, args = cli.parse_cli(arg_list)
ott_id_list, node_id_list = process_ott_and_node_id_list_args(args)
# use node_id_list if there are multiple. This is an odd call in the API
if (not node_id_list) and (not ott_id_list):
raise ValueError('Either --node-ids or --ott-ids must be provided.\n')
if len(ott_id_list) > 1 or (node_id_list and ott_id_list):
node_id_list.extend(['ott{}'.format(i) for i in ott_id_list])
ott_id_list.clear()
if len(node_id_list) == 1:
output = OT.synth_node_info(node_id=node_id_list[0],
include_lineage=args.include_lineage)
elif len(node_id_list) > 1:
output = OT.synth_node_info(node_ids=node_id_list,
include_lineage=args.include_lineage)
else:
assert len(ott_id_list) == 1
ott_id = ott_id_list[0]
assert ott_id is not None
output = OT.synth_node_info(ott_id=ott_id,
include_lineage=args.include_lineage)
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sp = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sp))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage='Look up a minimal context name of a set of names')
cli.parser.add_argument("names", nargs="+", help="names to match")
OT, args = cli.parse_cli(arg_list)
output = OT.tnrs_infer_context(args.names)
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sf = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sf))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage=
'Displays the searchable properties for studies and trees in the "phylesystem"'
)
OT = cli.parse_cli(arg_list)[0]
output = OT.studies_properties()
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sf = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sf))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage=
'Display node information about the Most Recent Common Ancestor of a set of IDs',
common_args=("ott-ids", "node-ids"))
OT, args = cli.parse_cli(arg_list)
ott_id_list, node_id_list = process_ott_and_node_id_list_args(args)
output = OT.synth_mrca(node_ids=node_id_list, ott_ids=ott_id_list)
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sp = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sp))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage=
'Display taxonomic information about the Most Recent Common Ancestor of a set of IDs',
common_args=("ott-ids", ))
OT, args = cli.parse_cli(arg_list)
ott_id_list = process_ott_and_node_id_list_args(args)[0]
if not ott_id_list:
sys.exit('--ott-ids must be provided.\n')
output = OT.taxon_mrca(ott_ids=ott_id_list)
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sf = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sf))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(usage='Display taxonomy and synthetic tree information '
'returned by the "about" API calls.',
common_args=("ott-ids", "node-ids"))
cli.parser.add_argument('--outfile', nargs='?', type=argparse.FileType('w'),
default=None)
OT, args = cli.parse_cli(arg_list)
ott_id_list, node_id_list = process_ott_and_node_id_list_args(args)
output = OT.synth_induced_tree(node_ids=node_id_list, ott_ids=ott_id_list)
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
sp = output.tree.as_ascii_plot()
out.write('{}\n'.format(sp))
if args.outfile is not None:
new = (output.response_dict['newick'])
args.outfile.write('{}\n'.format(new))
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage='Display taxonomy and synthetic tree information '
'returned by the "about" API calls.')
OT = cli.parse_cli()[0]
about = OT.about()
if list_for_results is not None:
list_for_results.append(about)
if out is None:
return 0
for k in about.keys():
call_record = about[k]
if call_record:
print(k)
sf = json.dumps(call_record,
sort_keys=True,
indent=2,
separators=(',', ': '),
ensure_ascii=True)
print(sf)
print('')
return 0
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage='Fetch a tree by its phylesystem study ID and tree ID')
cli.parser.add_argument(dest='study_id',
help="The ID of the study to retrieve")
cli.parser.add_argument(dest='tree_id',
help="The ID of the study to retrieve")
cli.parser.add_argument(
'--format',
default='nexson',
type=str,
help='one of: "newick", "nexson", "nexus", or "object"]')
OT, args = cli.parse_cli(arg_list)
output = OT.get_tree(args.study_id, args.tree_id, tree_format=args.format)
if list_for_results is not None:
list_for_results.append(output)
if out is None:
return 0
if args.format == 'nexson':
out.write('{}\n'.format(
json.dumps(output.response_dict, indent=2, sort_keys=True)))
else:
out.write('{}\n'.format(output.tree))
return 0
#!/usr/bin/env python3
import json
from opentree import OTCommandLineTool, get_suppressed_taxon_flag_expl_url
cli = OTCommandLineTool(usage='Look up the OTT IDs for a set of names')
cli.parser.add_argument("names", nargs="+", help="names to match")
cli.parser.add_argument(
"--context-name",
default=None,
help=
'If you know the named Open Tree name searching index, you can supply it here '
'to limit your search to only a subset of the taxonomny.')
cli.parser.add_argument("--do-approximate-matching",
action="store_true",
help='Enables fuzzy matching')
cli.parser.add_argument(
"--include-suppressed",
action="store_true",
help='Return taxa that are normally suppressed from TNRS '
'results. See {}'.format(get_suppressed_taxon_flag_expl_url()))
OT, args = cli.parse_cli()
output = OT.tnrs_match(args.names,
context_name=args.context_name,
do_approximate_matching=args.do_approximate_matching,
include_suppressed=args.include_suppressed)
print(json.dumps(output.response_dict, indent=2, sort_keys=True))
#!/usr/bin/env python3 import json from opentree import OTCommandLineTool cli = OTCommandLineTool(usage='Display the Open Tree TNRS named contexts') OT = cli.parse_cli()[0] output = OT.tnrs_contexts() print(json.dumps(output.response_dict, indent=2, sort_keys=True))
#!/usr/bin/env python3
import json
import sys
from opentree import OTCommandLineTool
cli = OTCommandLineTool(usage='Fetch a study by its phylesystem study ID')
cli.parser.add_argument(dest='study_id',
help="The ID of the study to retrieve")
OT, args = cli.parse_cli()
output = OT.get_study(args.study_id)
print(json.dumps(output.response_dict, indent=2, sort_keys=True))
sys.exit(0 if output else 1)
def main(arg_list, out, list_for_results=None):
cli = OTCommandLineTool(
usage=
'Gets a subtree of the synthetic tree rooted at the node requested',
common_args=("ott-id", "node-id"))
cli.parser.add_argument('--format',
default='newick',
help='"newick" or "arguson" tree format')
cli.parser.add_argument(
'--label-format',
default='name_and_id',
help='"name_and_id", "name", or "id" style of labeling newick nodes')
cli.parser.add_argument(
'--height-limit',
default=None,
type=int,
help='number of levels to return. -1 for unlimited (newick only)')
cli.parser.add_argument('--outfile',
nargs='?',
type=argparse.FileType('w'),
default=None)
OT, args = cli.parse_cli(arg_list)
tree_format = args.format.strip().lower()
if tree_format not in ["newick", "arguson"]:
raise RuntimeError(
"Did not recognize --format={}\n".format(tree_format))
if args.height_limit is None:
if tree_format == "newick":
height_limit = -1
else:
height_limit = 3
else:
height_limit = args.height_limit
if height_limit < -1:
raise RuntimeError('Expecting height limit to be >= -1.')
label_format = args.label_format.strip().lower()
if label_format not in ["name_and_id", "name", "id"]:
raise RuntimeError(
"Did not recognize --label-format={}\n".format(label_format))
ott_id, node_id = process_ott_or_node_id_arg(args)
# use node_id_list if there are multiple. This is an odd call in the API
if (ott_id is None) and (node_id is None):
raise RuntimeError(
'Either --node-ids or --ott-ids must be provided.\n')
if ott_id is not None:
output = OT.synth_subtree(ott_id=ott_id,
tree_format=tree_format,
label_format=label_format,
height_limit=height_limit)
else:
output = OT.synth_subtree(node_id=node_id,
tree_format=tree_format,
label_format=label_format,
height_limit=height_limit)
if list_for_results is not None:
list_for_results.append(output)
if out is not None:
if tree_format == 'newick':
sp = output.tree.as_ascii_plot()
out.write('{}\n'.format(sp))
new = (output.response_dict['newick'])
args.outfile.write('{}\n'.format(new))
else:
sf = json.dumps(output.response_dict, indent=2, sort_keys=True)
out.write('{}\n'.format(sp))
args.outfile.write('{}\n'.format(sf))
return 0
#!/usr/bin/env python3
from opentree import OTCommandLineTool, process_ott_and_node_id_list_args
cli = OTCommandLineTool(usage='Display taxonomy and synthetic tree information '
'returned by the "about" API calls.',
common_args=("ott-ids", "node-ids"))
OT, args = cli.parse_cli()
ott_id_list, node_id_list = process_ott_and_node_id_list_args(args)
output = OT.synth_induced_tree(node_ids=node_id_list, ott_ids=ott_id_list)
print(output.tree.as_ascii_plot())
#!/usr/bin/env python3
import sys
from opentree import OTCommandLineTool, process_ott_or_node_id_arg
cli = OTCommandLineTool(
usage='Gets a subtree of the synthetic tree rooted at the node requested',
common_args=("ott-id", "node-id"))
cli.parser.add_argument('--format',
default='newick',
help='"newick" or "arguson" tree format')
cli.parser.add_argument(
'--label-format',
default='name_and_id',
help='"name_and_id", "name", or "id" style of labeling newick nodes')
cli.parser.add_argument(
'--height-limit',
default=None,
type=int,
help='number of levels to return. -1 for unlimited (newick only)')
OT, args = cli.parse_cli()
tree_format = args.format.strip().lower()
if tree_format not in ["newick", "arguson"]:
sys.exit("Did not recognize --format={}\n".format(tree_format))
if args.height_limit is None:
if tree_format == "newick":
height_limit = -1
else:
height_limit = 3
else:
#!/usr/bin/env python3
import json
from opentree import OTCommandLineTool
cli = OTCommandLineTool(
usage=
'Displays the searchable properties for studies and trees in the "phylesystem"'
)
OT = cli.parse_cli()[0]
output = OT.studies_properties()
print(json.dumps(output.response_dict, indent=2, sort_keys=True))
#!/usr/bin/env python3
import sys
from opentree import OTCommandLineTool
cli = OTCommandLineTool(
usage='Display taxonomy and synthetic tree information '
'returned by the "about" API calls.')
OT = cli.parse_cli()[0]
about = OT.about()
for k in about.keys():
call_record = about[k]
if call_record:
print(k)
call_record.write_response(sys.stdout)
print('')
about_info = OT.about()
synth_tree_about = about_info['synth_tree_about']
synth_id = synth_tree_about['synth_id']
subproblem_scaffold = OT.get_subproblem_scaffold_tree(synth_id)
scaf_newick = subproblem_scaffold.response.text
subprob_size_dict = OT.get_subproblem_size_info(synth_id).response_dict
tree = OT.ws.to_object_converter.tree_from_newick(scaf_newick)
augment_nodes_with_ot_properties(tree)
scaffold_id_set = scaffold_tree_to_ott_id_set(tree)
subproblem_list = []
for synth_nd in tip_synth_node_info["lineage"]:
snid = synth_nd["node_id"]
if snid.startswith('ott'):
sn_ott_id = ott_str_as_int(snid)
if sn_ott_id in scaffold_id_set:
m = "subproblem: OTT={} unique_name={}".format(
sn_ott_id, synth_nd["taxon"]["unique_name"])
subproblem_list.append((m, sn_ott_id, synth_nd))
subproblem_list.reverse()
prompt_for_subproblem_exploration(synth_id, subproblem_list,
subprob_size_dict)
if __name__ == '__main__':
cli = OTCommandLineTool(
usage='Display node info for the synthetic tree node(s) requested',
common_args=("ott-id", ))
OT, parsed_args = cli.parse_cli()
main(parsed_args)
#!/usr/bin/env python3
import json
import sys
from opentree import OTCommandLineTool, process_ott_and_node_id_list_args
cli = OTCommandLineTool(
usage=
'Display taxonomic information about the Most Recent Common Ancestor of a set of IDs',
common_args=("ott-ids", ))
OT, args = cli.parse_cli()
ott_id_list = process_ott_and_node_id_list_args(args)[0]
if not ott_id_list:
sys.exit('--ott-ids must be provided.\n')
output = OT.taxon_mrca(ott_ids=ott_id_list)
print(json.dumps(output.response_dict, indent=2, sort_keys=True))
#!/usr/bin/env python3
import json
from opentree import OTCommandLineTool
cli = OTCommandLineTool(
usage=
'Look up trees in the "phylesystem" set of phylogenetic studies that are in the Open '
'system')
cli.parser.add_argument("value", help="The value of the property to match")
cli.parser.add_argument("--property",
default=None,
required=True,
help='The name of the field to search through.')
cli.parser.add_argument("--verbose",
action="store_true",
help='include meta-data in response')
cli.parser.add_argument("--exact",
action="store_true",
help='disables fuzzy matching')
OT, args = cli.parse_cli()
output = OT.find_trees(args.value,
search_property=args.property,
verbose=args.verbose,
exact=args.exact)
print(json.dumps(output.response_dict, indent=2, sort_keys=True))
#!/usr/bin/env python3
import json
from opentree import OTCommandLineTool, get_suppressed_taxon_flag_expl_url
cli = OTCommandLineTool(
usage='Return some names that start with the provided name.')
cli.parser.add_argument("name", help="name string to complete")
cli.parser.add_argument(
"--context-name",
default=None,
help=
'If you know the named Open Tree name searching index, you can supply it here '
'to limit your search to only a subset of the taxonomny.')
cli.parser.add_argument(
"--include-suppressed",
action="store_true",
help='Return taxa that are normally suppressed from TNRS '
'results. See {}'.format(get_suppressed_taxon_flag_expl_url()))
OT, args = cli.parse_cli()
output = OT.tnrs_autocomplete(args.name,
context_name=args.context_name,
include_suppressed=args.include_suppressed)
print(json.dumps(output.response_dict, indent=2, sort_keys=True))
#!/usr/bin/env python3
import json
from opentree import OTCommandLineTool
cli = OTCommandLineTool(usage='Look up a minimal context name of a set of names')
cli.parser.add_argument("names", nargs="+", help="names to match")
OT, args = cli.parse_cli()
output = OT.tnrs_infer_context(args.names)
print(json.dumps(output.response_dict, indent=2, sort_keys=True))
#!/usr/bin/env python3
import sys
import json
from opentree import OTCommandLineTool
cli = OTCommandLineTool(usage='Display taxonomic info (based on the Open Tree Taxonomy) for a taxon ID',
common_args=("ott-id", ))
cli.parser.add_argument('--source-id', default=None, type=str,
help='A source taxonomy id for the taxon of interest, in the form prefix:id, for'
' example ncbi:9443, irmng:11338. '
'Valid prefixes are currently ncbi, gbif, worms, if, and irmng. '
'Either ott_id or source_id must be given, but not both')
cli.parser.add_argument('--include-lineage', action='store_true',
help='Return the lineage of nodes back to the root of the tree')
cli.parser.add_argument('--include-children', action='store_true',
help='Return information about all the children of this taxon')
cli.parser.add_argument('--include-terminal-descendants', action='store_true',
help='Return a list of terminal OTT IDs that are descendants of this taxon')
OT, args = cli.parse_cli()
kwargs = {'include_children': args.include_children,
'include_lineage': args.include_lineage,
'include_terminal_descendants': args.include_terminal_descendants,
}
if args.ott_id:
o = args.ott_id if not args.ott_id.startswith('ott') else args.ott_id[3:]
try:
ott_id = int(o)
except:
sys.exit('Expecting each ott ID to be an integer or a string starting with "ott". '