本文整理汇总了Python中tree.Tree.run_bionj方法的典型用法代码示例。如果您正苦于以下问题：Python Tree.run_bionj方法的具体用法？Python Tree.run_bionj怎么用？Python Tree.run_bionj使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类tree.Tree的用法示例。
在下文中一共展示了Tree.run_bionj方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: TCSeqRec
# 需要导入模块: from tree import Tree [as 别名]
# 或者: from tree.Tree import run_bionj [as 别名]
#.........这里部分代码省略.........
)
os.remove('{0}/{1}.phy'.format(tmpdir, filename))
return self.tree
def get_bionj_tree(
self,
model=None,
datatype=None,
ncat=1,
optimise='n',
tmpdir='/tmp',
overwrite=True,
verbose=False,
):
if not overwrite and self.tree.newick:
print '{0}: Tree exists and overwrite set to false'.format(self.name)
return self.tree
self.Tree = Tree()
filename = self._write_temp_phylip(tmpdir=tmpdir, use_hashname=True)
print 'Running bionj on ' + str(self.name) + '...'
input_file = '{0}/{1}.phy'.format(tmpdir, filename)
if not model and not datatype: # quick-fix to allow specification of other
if self.datatype == 'dna': # models when calling phyml
model = 'GTR'
datatype = 'nt'
elif self.datatype == 'protein':
model = 'WAG'
datatype = 'aa'
else:
print 'I don\'t know this datatype: {0}'.format(self.datatype)
return
t = self.tree.run_bionj(
model,
input_file,
datatype,
ncat=ncat,
name=self.name,
optimise=optimise,
overwrite=overwrite,
verbose=verbose,
)
os.remove('{0}/{1}.phy'.format(tmpdir, filename))
return self.tree
def get_raxml_tree(self, tmpdir='/tmp', overwrite=True):
if not overwrite and self.tree.newick:
print '{0}: Tree exists and overwrite set to false'.format(self.name)
return self.tree
self.tree = Tree()
self._write_temp_phylip(tmpdir=tmpdir)
print 'Running raxml on ' + str(self.name) + '...'
input_file = '{0}/{1}.phy'.format(tmpdir, self.name)
if self.datatype == 'dna':
model = 'GTRGAMMA'
elif self.datatype == 'protein':
model = 'PROTGAMMAWAG'
else:
print 'I don\'t know this datatype: {0}'.format(self.datatype)
return
self.tree.run_raxml(model, input_file, self.name, tmpdir,
overwrite=overwrite)
os.remove('{0}/{1}.phy'.format(tmpdir, self.name))
if os.path.isfile('{0}/{1}.phy.reduced'.format(tmpdir,
self.name)):