def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if(opts.parallel):
tmp_dir='jobs/'
make_output_dir(tmp_dir)
asr_table, ci_table =run_asr_in_parallel(tree=opts.input_tree_fp,table=opts.input_trait_table_fp,asr_method=opts.asr_method,parallel_method=opts.parallel_method, num_jobs=opts.num_jobs,tmp_dir=tmp_dir,verbose=opts.verbose)
else:
#call the apporpriate ASR app controller
if(opts.asr_method == 'wagner'):
asr_table = wagner_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,HALT_EXEC=opts.debug)
elif(opts.asr_method == 'bayestraits'):
pass
elif(opts.asr_method == 'ace_ml'):
asr_table,ci_table = ace_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,'ML',HALT_EXEC=opts.debug)
elif(opts.asr_method == 'ace_pic'):
asr_table,ci_table = ace_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,'pic',HALT_EXEC=opts.debug)
elif(opts.asr_method == 'ace_reml'):
asr_table,ci_table = ace_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,'REML',HALT_EXEC=opts.debug)
#output the table to file
make_output_dir_for_file(opts.output_fp)
asr_table.writeToFile(opts.output_fp,sep='\t')
#output the CI file (unless the method is wagner)
if not (opts.asr_method == 'wagner'):
make_output_dir_for_file(opts.output_ci_fp)
ci_table.writeToFile(opts.output_ci_fp,sep='\t')
def main():
option_parser, opts, args =\
parse_command_line_parameters(**script_info)
if(opts.parallel):
tmp_dir='jobs/'
make_output_dir(tmp_dir)
asr_table, ci_table =run_asr_in_parallel(tree=opts.input_tree_fp,table=opts.input_trait_table_fp,asr_method=opts.asr_method,parallel_method=opts.parallel_method, num_jobs=opts.num_jobs,tmp_dir=tmp_dir,verbose=opts.verbose)
else:
#call the apporpriate ASR app controller
if(opts.asr_method == 'wagner'):
asr_table = wagner_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,HALT_EXEC=opts.debug)
elif(opts.asr_method == 'bayestraits'):
pass
elif(opts.asr_method == 'ace_ml'):
asr_table,ci_table = ace_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,'ML',HALT_EXEC=opts.debug)
elif(opts.asr_method == 'ace_pic'):
asr_table,ci_table = ace_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,'pic',HALT_EXEC=opts.debug)
elif(opts.asr_method == 'ace_reml'):
asr_table,ci_table = ace_for_picrust(opts.input_tree_fp,opts.input_trait_table_fp,'REML',HALT_EXEC=opts.debug)
#output the table to file
make_output_dir_for_file(opts.output_fp)
asr_table.writeToFile(opts.output_fp,sep='\t')
#output the CI file (unless the method is wagner)
if not (opts.asr_method == 'wagner'):
make_output_dir_for_file(opts.output_ci_fp)
ci_table.writeToFile(opts.output_ci_fp,sep='\t')
def test_ace_for_picrust_ml(self):
""" test_ace_for_picrust with method 'ML' functions as expected with valid input
"""
actual, actual_ci = ace_for_picrust(self.in_tree1_fp, self.in_trait1_fp, method="ML")
expected = Table(
["nodes", "trait1", "trait2"],
[
["14", "2.9737", "2.5436"],
["12", "2.3701", "2.7056"],
["11", "0.8370", "2.9706"],
["10", "4.4826", "2.1388"],
],
)
self.assertEqual(actual.tostring(), expected.tostring())
expected_ci = Table(
["nodes", "trait1", "trait2"],
[
["14", "1.4467|4.5007", "2.1979|2.8894"],
["12", "0.9729|3.7674", "2.3892|3.0219"],
["11", "0.147|1.527", "2.8143|3.1268"],
["10", "3.4227|5.5426", "1.8988|2.3788"],
["sigma", "1.9742|0.6981", "0.1012|0.0359"],
["loglik", "-6.7207", "5.1623"],
],
)
self.assertEqual(actual_ci.tostring(), expected_ci.tostring())
def test_ace_for_picrust_pic_with_funky_tip_labels(self):
""" test_ace_for_picrust for a tree with underscores in tip labels
"""
actual, ci = ace_for_picrust(self.in_tree2_fp, self.in_trait3_fp, method="pic")
expected = Table(
["nodes", "trait1", "trait2"],
[["14", "2.9737", "2.5436"], ["12", "1.2727", "3"], ["11", "0.6667", "3"], ["10", "5", "2"]],
)
self.assertEqual(actual.tostring(), expected.tostring())
def test_ace_for_picrust_pic_with_funky_tip_labels(self):
""" test_ace_for_picrust for a tree with underscores in tip labels
"""
actual, ci = ace_for_picrust(self.in_tree2_fp,
self.in_trait3_fp,
method="pic")
expected = Table(['nodes', 'trait1', 'trait2'],
[['14', '2.9737', '2.5436'], ['12', '1.2727', '3'],
['11', '0.6667', '3'], ['10', '5', '2']])
self.assertEqual(actual.tostring(), expected.tostring())
def test_ace_for_picrust_pic_single_trait(self):
""" test_ace_for_picrust with method 'pic' functions as expected with single column trait table
"""
actual, ci = ace_for_picrust(self.in_tree1_fp,
self.in_trait2_fp,
method="pic")
expected = Table(['nodes', 'trait1'],
[['14', '2.9737'], ['12', '1.2727'], ['11', '0.6667'],
['10', '5']])
self.assertEqual(actual.tostring(), expected.tostring())
def test_ace_for_picrust_pic(self):
""" test_ace_for_picrust with method 'pic' functions as expected with valid input
"""
actual,actual_ci= ace_for_picrust(self.in_tree1_fp,self.in_trait1_fp, method="pic")
expected=Table(['nodes','trait1','trait2'],[['14','2.9737','2.5436'],['12','1.2727','3'],['11','0.6667','3'],['10','5','2']])
self.assertEqual(actual.tostring(),expected.tostring())
expected_ci=Table(['nodes','trait1','trait2'],\
[['14','0.7955|5.1519','0.3655|4.7218'],\
['12','-1.1009|3.6464','0.6264|5.3736'],\
['11','-0.4068|1.7402','1.9265|4.0735'],\
['10','3.3602|6.6398','0.3602|3.6398'],\
])
self.assertEqual(actual_ci.tostring(),expected_ci.tostring())
def test_ace_for_picrust_pic(self):
""" test_ace_for_picrust with method 'pic' functions as expected with valid input
"""
actual,actual_ci= ace_for_picrust(self.in_tree1_fp,self.in_trait1_fp, method="pic")
expected=Table(['nodes','trait1','trait2'],[['14','2.9737','2.5436'],['12','1.2727','3'],['11','0.6667','3'],['10','5','2']])
self.assertEqual(actual.tostring(),expected.tostring())
expected_ci=Table(['nodes','trait1','trait2'],\
[['14','0.7955|5.1519','0.3655|4.7218'],\
['12','-1.1009|3.6464','0.6264|5.3736'],\
['11','-0.4068|1.7402','1.9265|4.0735'],\
['10','3.3602|6.6398','0.3602|3.6398'],\
])
self.assertEqual(actual_ci.tostring(),expected_ci.tostring())
def test_ace_for_picrust_ml(self):
""" test_ace_for_picrust with method 'ML' functions as expected with valid input
"""
actual,actual_ci= ace_for_picrust(self.in_tree1_fp, self.in_trait1_fp, method="ML")
expected=Table(['nodes','trait1','trait2'],[['14','2.9737','2.5436'],['12','2.3701','2.7056'],['11','0.8370','2.9706'],['10','4.4826','2.1388']])
self.assertEqual(actual.tostring(),expected.tostring())
expected_ci=Table(['nodes','trait1','trait2'],\
[['14','1.4467|4.5007','2.1979|2.8894'],\
['12','0.9729|3.7674','2.3892|3.0219'],\
['11','0.147|1.527','2.8143|3.1268'],\
['10','3.4227|5.5426','1.8988|2.3788'],\
['sigma','1.9742|0.6981','0.1012|0.0359'],\
['loglik','-6.7207','5.1623'],\
])
self.assertEqual(actual_ci.tostring(),expected_ci.tostring())
def test_ace_for_picrust_ml(self):
""" test_ace_for_picrust with method 'ML' functions as expected with valid input
"""
actual,actual_ci= ace_for_picrust(self.in_tree1_fp, self.in_trait1_fp, method="ML")
expected=Table(['nodes','trait1','trait2'],[['14','2.9737','2.5436'],['12','2.3701','2.7056'],['11','0.8370','2.9706'],['10','4.4826','2.1388']])
self.assertEqual(actual.tostring(),expected.tostring())
expected_ci=Table(['nodes','trait1','trait2'],\
[['14','1.4467|4.5007','2.1979|2.8894'],\
['12','0.9729|3.7674','2.3892|3.0219'],\
['11','0.147|1.527','2.8143|3.1268'],\
['10','3.4227|5.5426','1.8988|2.3788'],\
['sigma','1.9742|0.6981','0.1012|0.0359'],\
['loglik','-6.7207','5.1623'],\
])
self.assertEqual(actual_ci.tostring(),expected_ci.tostring())
def test_ace_for_picrust_pic(self):
""" test_ace_for_picrust with method 'pic' functions as expected with valid input
"""
actual, actual_ci = ace_for_picrust(self.in_tree1_fp, self.in_trait1_fp, method="pic")
expected = Table(
["nodes", "trait1", "trait2"],
[["14", "2.9737", "2.5436"], ["12", "1.2727", "3"], ["11", "0.6667", "3"], ["10", "5", "2"]],
)
self.assertEqual(actual.tostring(), expected.tostring())
expected_ci = Table(
["nodes", "trait1", "trait2"],
[
["14", "0.7955|5.1519", "0.3655|4.7218"],
["12", "-1.1009|3.6464", "0.6264|5.3736"],
["11", "-0.4068|1.7402", "1.9265|4.0735"],
["10", "3.3602|6.6398", "0.3602|3.6398"],
],
)
self.assertEqual(actual_ci.tostring(), expected_ci.tostring())
def test_ace_for_picrust_pic_single_trait(self):
""" test_ace_for_picrust with method 'pic' functions as expected with single column trait table
"""
actual,ci= ace_for_picrust(self.in_tree1_fp,self.in_trait2_fp, method="pic")
expected=Table(['nodes','trait1'],[['14','2.9737'],['12','1.2727'],['11','0.6667'],['10','5']])
self.assertEqual(actual.tostring(),expected.tostring())
def test_ace_for_picrust_pic_with_funky_tip_labels(self):
""" test_ace_for_picrust for a tree with underscores in tip labels
"""
actual,ci= ace_for_picrust(self.in_tree2_fp,self.in_trait3_fp, method="pic")
expected=Table(['nodes','trait1','trait2'],[['14','2.9737','2.5436'],['12','1.2727','3'],['11','0.6667','3'],['10','5','2']])
self.assertEqual(actual.tostring(),expected.tostring())
def test_ace_for_picrust_pic_single_trait(self):
""" test_ace_for_picrust with method 'pic' functions as expected with single column trait table
"""
actual, ci = ace_for_picrust(self.in_tree1_fp, self.in_trait2_fp, method="pic")
expected = Table(["nodes", "trait1"], [["14", "2.9737"], ["12", "1.2727"], ["11", "0.6667"], ["10", "5"]])
self.assertEqual(actual.tostring(), expected.tostring())