def testMimicPhylesystemExport(self):
study_nexson = pathmap.nexson_obj('10/pg_10.json')
src_schema = PhyloSchema('nexson', version='1.2.1')
out_schema = PhyloSchema(schema='newick', content='tree', content_id='bogusID here')
result_data = out_schema.convert(study_nexson, serialize=True, src_schema=src_schema)
self.assertFalse(bool(result_data))
out_schema = PhyloSchema(schema='nexus', content='tree', content_id='bogusID here')
result_data = out_schema.convert(study_nexson, serialize=True, src_schema=src_schema)
self.assertFalse(bool(result_data))
def testNewickConvStudyViaPS(self):
o = pathmap.nexson_obj('9/v1.2.json')
ps = PhyloSchema(type_ext='.tre')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('(')) # pylint: disable=E1103
def testNexusConvStudyViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nex')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNexusConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexus', content='tree', content_id='tree3')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNewickConvStudyViaPS(self):
o = pathmap.nexson_obj('9/v1.2.json')
ps = PhyloSchema(type_ext='.tre')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('(')) # pylint: disable=E1103
def testNexusConvStudyViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema(type_ext='.nex')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def testNexusConvViaPS(self):
o = pathmap.nexson_obj('10/pg_10.json')
ps = PhyloSchema('nexus', content='tree', content_id='tree3')
nex = ps.convert(o, serialize=True)
self.assertTrue(nex.startswith('#')) # pylint: disable=E1103
def _main():
import sys, codecs, json
import argparse
_HELP_MESSAGE = '''NexSON (or NeXML) to newick converter'''
_EPILOG = '''UTF-8 encoding is used (for input and output).
Environmental variables used:
NEXSON_LOGGING_LEVEL logging setting: NotSet, Debug, Warn, Info, Error
NEXSON_LOGGING_FORMAT format string for logging messages.
'''
tip_label_list = PhyloSchema._otu_label_list
for tl in tip_label_list:
assert(tl.startswith('ot:'))
tip_labels_choices = [i[3:] for i in tip_label_list]
parser = argparse.ArgumentParser(description=_HELP_MESSAGE,
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog=_EPILOG)
parser.add_argument("input", help="filepath to input")
parser.add_argument("-i", "--id",
metavar="TREE-ID",
required=False,
help="The ID tree to emit")
parser.add_argument("-o", "--output",
metavar="FILE",
required=False,
help="output filepath. Standard output is used if omitted.")
parser.add_argument("-l", "--list",
action="store_true",
default=False,
help="Just list the tree IDs in the nexSON.")
parser.add_argument("-x", "--xml",
action="store_true",
default=False,
help="Parse input as NeXML rather than NexSON.")
tl_help = 'The field to use to label tips. Should be one of: "{}"'
tl_help = tl_help.format('", "'.join(tip_labels_choices))
parser.add_argument("-t", "--tip-label",
metavar="STRING",
required=False,
default='originallabel',
help=tl_help)
args = parser.parse_args()
otu_label = args.tip_label.lower()
if not otu_label.startswith('ot:'):
otu_label = 'ot:' + otu_label
if otu_label not in tip_label_list:
sys.exit('Illegal tip label choice "{}"\n'.format(args.tip_label))
inpfn = args.input
outfn = args.output
try:
inp = codecs.open(inpfn, mode='rU', encoding='utf-8')
except:
sys.exit('nexson_newick: Could not open file "{fn}"\n'.format(fn=inpfn))
if outfn is not None:
try:
out = codecs.open(outfn, mode='w', encoding='utf-8')
except:
sys.exit('nexson_newick: Could not open output filepath "{fn}"\n'.format(fn=outfn))
else:
out = codecs.getwriter('utf-8')(sys.stdout)
if args.xml:
src_schema = PhyloSchema('nexml')
blob = get_ot_study_info_from_nexml(inp)
else:
src_schema = None
blob = json.load(inp)
if args.list:
schema = PhyloSchema(content='treelist', output_nexml2json='1.2.1')
tl = schema.convert(src=blob, src_schema=src_schema)
out.write('{t}\n'.format(t='\n'.join(tl)))
else:
schema = create_content_spec(content='tree', content_id=args.id, format='newick', otu_label=otu_label)
try:
schema.convert(src=blob, serialize=True, output_dest=out, src_schema=src_schema)
except KeyError:
if 'nexml' not in blob and 'nex:nexml' not in blob:
blob = blob['data']
schema.convert(src=blob, serialize=True, output_dest=out, src_schema=src_schema)
else:
raise
