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import os
import sys
import StringIO
import unittest
from Bio.Nexus import Nexus
def run_tests(argv):
test_suite = testing_suite()
runner = unittest.TextTestRunner(sys.stdout, verbosity = 2)
runner.run(test_suite)
def testing_suite():
"""Generate the suite of tests."""
test_suite = unittest.TestSuite()
test_loader = unittest.TestLoader()
test_loader.testMethodPrefix = 't_'
tests = [NexusTest1]
for test in tests:
cur_suite = test_loader.loadTestsFromTestCase(test)
test_suite.addTest(cur_suite)
return test_suite
class NexusTest1(unittest.TestCase):
def setUp(self):
self.handle = open("Nexus/test_Nexus_input.nex")
def tearDown(self):
self.handle.close()
def print_dictnlist(self,name,d):
"""Output a list or a dict alphabetically by keys()"""
if type(d)==dict:
dk=d.keys()
dk.sort()
print '\n%s:\n%s' % (name, '\n'.join([str(k)+'\t'+str(d[k]) for k in dk]))
else:
print '\n%s:\n%s' % (name, '\n'.join([k for k in d]))
def output_basics(self,n):
"""Output basic info of a nexus file."""
# When run on Windows, want to match the expected test output
# (in file output/test_Nexus) which uses "Nexus/f1.nex", not "Nexus\f1.nex"
print '\nName:',n.filename.replace(os.sep,"/")
print '\n',n.ntax, n.nchar, n.datatype, n.interleave, n.missing, n.gap
self.print_dictnlist('Taxa',n.taxlabels)
self.print_dictnlist('Charlabels',n.charlabels)
self.print_dictnlist('Charsets',n.charsets)
self.print_dictnlist('Taxsets',n.taxsets)
ps=n.charpartitions.keys()
ps.sort()
print '\nCharpartitions:'
for pk in ps:
self.print_dictnlist(pk,n.charpartitions[pk])
ps=n.taxpartitions.keys()
ps.sort()
print '\nTaxpartitions:'
for pk in ps:
self.print_dictnlist(pk,n.taxpartitions[pk])
def t_NexusTest1(self):
"""Test Nexus module"""
n=Nexus.Nexus(self.handle)
# check data of main nexus file
self.output_basics(n)
# now we check excluding characters, deleting taxa, and exporting adjusted sets
f1=os.path.join('Nexus','f1.nex')
f2=os.path.join('Nexus','f2.nex')
n.write_nexus_data(f1,delete=['t1','t7'],exclude=n.invert(n.charsets['big']))
n.write_nexus_data(f2,delete=['t2_the_name'],exclude=range(3,40,4))
nf1=Nexus.Nexus(f1)
self.output_basics(nf1)
nf2=Nexus.Nexus(f2)
self.output_basics(nf2)
# check the stepmatrix
print n.weighted_stepmatrix(name='matrix_test')
def t_TreeTest1(self):
"""Test Tree module."""
n=Nexus.Nexus(self.handle)
t3=n.trees[2]
t2=n.trees[2]
t3.root_with_outgroup(['t1','t5'])
print t3
print 'Monophyletic t6,t7,t8,t9:',t3.is_monophyletic(['t8','t9','t6','t7'])
print 'Monophyletic t1,t5:',t3.is_monophyletic(['t1','t5'])
print 'Subtree t1,t5:',t3.set_subtree(t3.is_monophyletic(['t1','t5']))
t3.split(parent_id=t3.search_taxon('t9'))
print 'The tree looks as follows:'
t3.display()
print 'self incompatibility...:',t3.is_compatible(t2,threshold=0.3)
if __name__ == "__main__":
sys.exit(run_tests(sys.argv))
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