index
int64 0
731k
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98
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stringlengths 1
76
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stringlengths 0
281k
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720,768
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ete3.nexml._nexml
|
insert_meta
| null |
def insert_meta(self, index, value): self.meta[index] = value
|
(self, index, value)
|
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] |
720,769
|
ete3.nexml._nexml
|
insert_otus
| null |
def insert_otus(self, index, value): self.otus[index] = value
|
(self, index, value)
|
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720,770
|
ete3.nexml._nexml
|
insert_trees
| null |
def insert_trees(self, index, value): self.trees[index] = value
|
(self, index, value)
|
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720,771
|
ete3.nexml._nexml
|
set_about
| null |
def set_about(self, about): self.about = about
|
(self, about)
|
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720,772
|
ete3.nexml._nexml
|
set_anyAttributes_
| null |
def set_anyAttributes_(self, anyAttributes_): self.anyAttributes_ = anyAttributes_
|
(self, anyAttributes_)
|
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] |
720,773
|
ete3.nexml._nexml
|
set_characters
| null |
def set_characters(self, characters): self.characters = characters
|
(self, characters)
|
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720,774
|
ete3.nexml._nexml
|
set_generator
| null |
def set_generator(self, generator): self.generator = generator
|
(self, generator)
|
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720,775
|
ete3.nexml._nexml
|
set_meta
| null |
def set_meta(self, meta): self.meta = meta
|
(self, meta)
|
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] |
720,776
|
ete3.nexml._nexml
|
set_otus
| null |
def set_otus(self, otus): self.otus = otus
|
(self, otus)
|
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0.044853080064058304,
-0.04412629082798958,
-0.06561839580535889
] |
720,777
|
ete3.nexml._nexml
|
set_trees
| null |
def set_trees(self, trees): self.trees = trees
|
(self, trees)
|
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720,778
|
ete3.nexml._nexml
|
set_version
| null |
def set_version(self, version): self.version = version
|
(self, version)
|
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] |
720,779
|
ete3.nexml._nexml
|
validate_Nexml1_0
| null |
def validate_Nexml1_0(self, value):
# Validate type Nexml1_0, a restriction on xs:decimal.
pass
|
(self, value)
|
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] |
720,780
|
ete3.nexml._nexml_tree
|
NexmlTree
|
Special PhyloTree object with nexml support
|
class NexmlTree(PhyloTree):
"""
Special PhyloTree object with nexml support
"""
def __repr__(self):
return "NexML ETE tree <%s>" %hex(hash(self))
def _get_dist(self):
return self.nexml_edge.get_length()
def _set_dist(self, value):
try:
self.nexml_edge.set_length(value)
except ValueError:
raise
def _get_support(self):
return self._nexml_support.content
def _set_support(self, value):
try:
self._nexml_support.content = float(value)
except ValueError:
raise
def _get_name(self):
return self.nexml_node.get_label()
def _set_name(self, value):
try:
self.nexml_node.set_label(value)
except ValueError:
raise
def _get_children(self):
return self._children
def _set_children(self, value):
if isinstance(value, Children) and \
len(set([type(n)==type(self) for n in value]))<2:
self._children = value
else:
raise ValueError("children:wrong type")
dist = property(fget=_get_dist, fset=_set_dist)
support = property(fget=_get_support, fset=_set_support)
children = property(fget=_get_children, fset=_set_children)
name = property(fget=_get_name, fset=_set_name)
def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0):
self.nexml_tree = FloatTree()
self.nexml_tree.set_anyAttributes_({'xsi:type': 'FloatTree'})
self.nexml_node = TreeNode()
self.nexml_edge = TreeFloatEdge()
self.nexml_node.id = "node_%s" %hash(self)
self.nexml_edge.id = "edge_%s" %hash(self)
self.nexml_project = None
self._nexml_support = LiteralMeta(datatype="float", property="branch_support", content=1.0)
self.nexml_edge.length = 0.0
self.nexml_edge.add_meta(self._nexml_support)
# Initialize empty PhyloTree
super(NexmlTree, self).__init__()
self._children = Children()
self._children.node = self
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
read_newick(newick, root_node=self, format=format)
self.set_species_naming_function(sp_naming_function)
def set_nexml_project(self, nexml_obj):
self.nexml_project = nexml_obj
def build(self, node):
self.nexml_tree = FloatTree()
tree = self.nexml_tree
tree.build(node)
# This detects the outgroup of the tree even if the root tag
# is not set in any node
rootid = set([e.source for e in tree.edge]) - set([e.target for e in tree.edge])
nodeid2node = {rootid.pop(): self}
for xmledge in tree.edge:
child = nodeid2node.setdefault(xmledge.target, self.__class__() )
parent = nodeid2node.setdefault(xmledge.source, self.__class__() )
child.name = xmledge.target
child.nexml_node.id = xmledge.target
parent.name = xmledge.source
parent.nexml_node.id = xmledge.source
child.nexml_edge = xmledge
if xmledge.length is not None:
child.dist = float(xmledge.length)
parent.add_child(child)
for xmlnode in tree.node:
# just a warning. I don't know if this can occur
if xmlnode.id not in nodeid2node:
print("Unused node", xmlnode.id, file=sys.stderr)
continue
ete_node = nodeid2node[xmlnode.id]
ete_node.nexml_node = xmlnode
if xmlnode.label:
ete_node.name = xmlnode.label
elif xmlnode.id is not None:
ete_node.name = xmlnode.id
def export(self, outfile=sys.stdout, level=0, namespace_='', name_='FloatTree', namespacedef_=''):
if self.nexml_tree:
info = [(n.nexml_edge, n.nexml_node) for n in self.traverse()]
self.nexml_node.set_root(True)
self.nexml_tree.set_edge([i[0] for i in info])
self.nexml_tree.set_node([i[1] for i in info])
self.nexml_tree.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
def exportChildren(self, outfile, level, namespace_='', name_='FloatTree'):
sorted_nodes = []
sorted_edges = []
for n in self.traverse():
# process node
node_obj = self.mixedclass_(MixedContainer.CategoryComplex,
MixedContainer.TypeNone, 'node', n.nexml_node)
sorted_nodes.append(node_obj)
# process edge
if n.nexml_edge:
edge_obj = self.mixedclass_(MixedContainer.CategoryComplex,
MixedContainer.TypeNone, 'edge', n.nexml_edge)
sorted_edges.append(edge_obj)
# process the nodes and edges
self.tree.content_ = sorted_nodes + sorted_edges
for item_ in self.tree.content_:
item_.export(outfile, level, item_.name, namespace_)
|
(newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0)
|
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0.04766593500971794
] |
720,786
|
ete3.nexml._nexml_tree
|
__init__
| null |
def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0):
self.nexml_tree = FloatTree()
self.nexml_tree.set_anyAttributes_({'xsi:type': 'FloatTree'})
self.nexml_node = TreeNode()
self.nexml_edge = TreeFloatEdge()
self.nexml_node.id = "node_%s" %hash(self)
self.nexml_edge.id = "edge_%s" %hash(self)
self.nexml_project = None
self._nexml_support = LiteralMeta(datatype="float", property="branch_support", content=1.0)
self.nexml_edge.length = 0.0
self.nexml_edge.add_meta(self._nexml_support)
# Initialize empty PhyloTree
super(NexmlTree, self).__init__()
self._children = Children()
self._children.node = self
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
read_newick(newick, root_node=self, format=format)
self.set_species_naming_function(sp_naming_function)
|
(self, newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0)
|
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720,790
|
ete3.nexml._nexml_tree
|
__repr__
| null |
def __repr__(self):
return "NexML ETE tree <%s>" %hex(hash(self))
|
(self)
|
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720,795
|
ete3.nexml._nexml_tree
|
_get_dist
| null |
def _get_dist(self):
return self.nexml_edge.get_length()
|
(self)
|
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] |
720,798
|
ete3.nexml._nexml_tree
|
_get_name
| null |
def _get_name(self):
return self.nexml_node.get_label()
|
(self)
|
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] |
720,801
|
ete3.nexml._nexml_tree
|
_get_support
| null |
def _get_support(self):
return self._nexml_support.content
|
(self)
|
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] |
720,806
|
ete3.nexml._nexml_tree
|
_set_children
| null |
def _set_children(self, value):
if isinstance(value, Children) and \
len(set([type(n)==type(self) for n in value]))<2:
self._children = value
else:
raise ValueError("children:wrong type")
|
(self, value)
|
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] |
720,807
|
ete3.nexml._nexml_tree
|
_set_dist
| null |
def _set_dist(self, value):
try:
self.nexml_edge.set_length(value)
except ValueError:
raise
|
(self, value)
|
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] |
720,809
|
ete3.nexml._nexml_tree
|
_set_name
| null |
def _set_name(self, value):
try:
self.nexml_node.set_label(value)
except ValueError:
raise
|
(self, value)
|
[
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] |
720,812
|
ete3.nexml._nexml_tree
|
_set_support
| null |
def _set_support(self, value):
try:
self._nexml_support.content = float(value)
except ValueError:
raise
|
(self, value)
|
[
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] |
720,820
|
ete3.nexml._nexml_tree
|
build
| null |
def build(self, node):
self.nexml_tree = FloatTree()
tree = self.nexml_tree
tree.build(node)
# This detects the outgroup of the tree even if the root tag
# is not set in any node
rootid = set([e.source for e in tree.edge]) - set([e.target for e in tree.edge])
nodeid2node = {rootid.pop(): self}
for xmledge in tree.edge:
child = nodeid2node.setdefault(xmledge.target, self.__class__() )
parent = nodeid2node.setdefault(xmledge.source, self.__class__() )
child.name = xmledge.target
child.nexml_node.id = xmledge.target
parent.name = xmledge.source
parent.nexml_node.id = xmledge.source
child.nexml_edge = xmledge
if xmledge.length is not None:
child.dist = float(xmledge.length)
parent.add_child(child)
for xmlnode in tree.node:
# just a warning. I don't know if this can occur
if xmlnode.id not in nodeid2node:
print("Unused node", xmlnode.id, file=sys.stderr)
continue
ete_node = nodeid2node[xmlnode.id]
ete_node.nexml_node = xmlnode
if xmlnode.label:
ete_node.name = xmlnode.label
elif xmlnode.id is not None:
ete_node.name = xmlnode.id
|
(self, node)
|
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] |
720,832
|
ete3.nexml._nexml_tree
|
export
| null |
def export(self, outfile=sys.stdout, level=0, namespace_='', name_='FloatTree', namespacedef_=''):
if self.nexml_tree:
info = [(n.nexml_edge, n.nexml_node) for n in self.traverse()]
self.nexml_node.set_root(True)
self.nexml_tree.set_edge([i[0] for i in info])
self.nexml_tree.set_node([i[1] for i in info])
self.nexml_tree.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
|
(self, outfile=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, level=0, namespace_='', name_='FloatTree', namespacedef_='')
|
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] |
720,833
|
ete3.nexml._nexml_tree
|
exportChildren
| null |
def exportChildren(self, outfile, level, namespace_='', name_='FloatTree'):
sorted_nodes = []
sorted_edges = []
for n in self.traverse():
# process node
node_obj = self.mixedclass_(MixedContainer.CategoryComplex,
MixedContainer.TypeNone, 'node', n.nexml_node)
sorted_nodes.append(node_obj)
# process edge
if n.nexml_edge:
edge_obj = self.mixedclass_(MixedContainer.CategoryComplex,
MixedContainer.TypeNone, 'edge', n.nexml_edge)
sorted_edges.append(edge_obj)
# process the nodes and edges
self.tree.content_ = sorted_nodes + sorted_edges
for item_ in self.tree.content_:
item_.export(outfile, level, item_.name, namespace_)
|
(self, outfile, level, namespace_='', name_='FloatTree')
|
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] |
720,874
|
ete3.phylo.phylotree
|
link_to_alignment
| null |
def link_to_alignment(self, alignment, alg_format="fasta", **kwargs):
missing_leaves = []
missing_internal = []
if type(alignment) == SeqGroup:
alg = alignment
else:
alg = SeqGroup(alignment, format=alg_format, **kwargs)
# sets the seq of
for n in self.traverse():
try:
n.add_feature("sequence",alg.get_seq(n.name))
except KeyError:
if n.is_leaf():
missing_leaves.append(n.name)
else:
missing_internal.append(n.name)
if len(missing_leaves)>0:
print("Warnning: [%d] terminal nodes could not be found in the alignment." %\
len(missing_leaves), file=sys.stderr)
# Show warning of not associated internal nodes.
# if len(missing_internal)>0:
# print >>sys.stderr, \
# "Warnning: [%d] internal nodes could not be found in the alignment." %\
# len(missing_leaves)
|
(self, alignment, alg_format='fasta', **kwargs)
|
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] |
720,886
|
ete3.nexml._nexml_tree
|
set_nexml_project
| null |
def set_nexml_project(self, nexml_obj):
self.nexml_project = nexml_obj
|
(self, nexml_obj)
|
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720,898
|
ete3.phylo.phylotree
|
PhyloNode
|
.. currentmodule:: ete3
Extends the standard :class:`TreeNode` instance. It adds
specific attributes and methods to work with phylogentic trees.
:argument newick: Path to the file containing the tree or, alternatively,
the text string containing the same information.
:argument alignment: file containing a multiple sequence alignment.
:argument alg_format: "fasta", "phylip" or "iphylip" (interleaved)
:argument format: sub-newick format
.. table::
====== ==============================================
FORMAT DESCRIPTION
====== ==============================================
0 flexible with support values
1 flexible with internal node names
2 all branches + leaf names + internal supports
3 all branches + all names
4 leaf branches + leaf names
5 internal and leaf branches + leaf names
6 internal branches + leaf names
7 leaf branches + all names
8 all names
9 leaf names
100 topology only
====== ==============================================
:argument sp_naming_function: Pointer to a parsing python
function that receives nodename as first argument and returns
the species name (see
:func:`PhyloNode.set_species_naming_function`. By default, the
3 first letter of nodes will be used as species identifiers.
:returns: a tree node object which represents the base of the tree.
|
class PhyloNode(TreeNode):
"""
.. currentmodule:: ete3
Extends the standard :class:`TreeNode` instance. It adds
specific attributes and methods to work with phylogentic trees.
:argument newick: Path to the file containing the tree or, alternatively,
the text string containing the same information.
:argument alignment: file containing a multiple sequence alignment.
:argument alg_format: "fasta", "phylip" or "iphylip" (interleaved)
:argument format: sub-newick format
.. table::
====== ==============================================
FORMAT DESCRIPTION
====== ==============================================
0 flexible with support values
1 flexible with internal node names
2 all branches + leaf names + internal supports
3 all branches + all names
4 leaf branches + leaf names
5 internal and leaf branches + leaf names
6 internal branches + leaf names
7 leaf branches + all names
8 all names
9 leaf names
100 topology only
====== ==============================================
:argument sp_naming_function: Pointer to a parsing python
function that receives nodename as first argument and returns
the species name (see
:func:`PhyloNode.set_species_naming_function`. By default, the
3 first letter of nodes will be used as species identifiers.
:returns: a tree node object which represents the base of the tree.
"""
def _get_species(self):
if self._speciesFunction:
try:
return self._speciesFunction(self.name)
except:
return self._speciesFunction(self)
else:
return self._species
def _set_species(self, value):
if self._speciesFunction:
pass
else:
self._species = value
# This tweak overwrites the native 'name' attribute to create a
# property that updates the species code every time name is
# changed
#: .. currentmodule:: ete3
#:
#Species code associated to the node. This property can be
#automatically extracted from the TreeNode.name attribute or
#manually set (see :func:`PhyloNode.set_species_naming_function`).
species = property(fget = _get_species, fset = _set_species)
def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0, **kargs):
# _update names?
self._name = "NoName"
self._species = "Unknown"
self._speciesFunction = None
# Caution! native __init__ has to be called after setting
# _speciesFunction to None!!
TreeNode.__init__(self, newick=newick, format=format, **kargs)
# This will be only executed after reading the whole tree,
# because the argument 'alignment' is not passed to the
# PhyloNode constructor during parsing
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
self.set_species_naming_function(sp_naming_function)
def __repr__(self):
return "PhyloTree node '%s' (%s)" %(self.name, hex(self.__hash__()))
def set_species_naming_function(self, fn):
"""
Sets the parsing function used to extract species name from a
node's name.
:argument fn: Pointer to a parsing python function that
receives nodename as first argument and returns the species
name.
::
# Example of a parsing function to extract species names for
# all nodes in a given tree.
def parse_sp_name(node_name):
return node_name.split("_")[1]
tree.set_species_naming_function(parse_sp_name)
"""
if fn:
for n in self.traverse():
n._speciesFunction = fn
if n.is_leaf():
n.features.add("species")
def link_to_alignment(self, alignment, alg_format="fasta", **kwargs):
missing_leaves = []
missing_internal = []
if type(alignment) == SeqGroup:
alg = alignment
else:
alg = SeqGroup(alignment, format=alg_format, **kwargs)
# sets the seq of
for n in self.traverse():
try:
n.add_feature("sequence",alg.get_seq(n.name))
except KeyError:
if n.is_leaf():
missing_leaves.append(n.name)
else:
missing_internal.append(n.name)
if len(missing_leaves)>0:
print("Warnning: [%d] terminal nodes could not be found in the alignment." %\
len(missing_leaves), file=sys.stderr)
# Show warning of not associated internal nodes.
# if len(missing_internal)>0:
# print >>sys.stderr, \
# "Warnning: [%d] internal nodes could not be found in the alignment." %\
# len(missing_leaves)
def get_species(self):
""" Returns the set of species covered by its partition. """
return set([l.species for l in self.iter_leaves()])
def iter_species(self):
""" Returns an iterator over the species grouped by this node. """
spcs = set([])
for l in self.iter_leaves():
if l.species not in spcs:
spcs.add(l.species)
yield l.species
def get_age(self, species2age):
"""
Implements the phylostratigrafic method described in:
Huerta-Cepas, J., & Gabaldon, T. (2011). Assigning duplication events to
relative temporal scales in genome-wide studies. Bioinformatics, 27(1),
38-45.
"""
return max([species2age[sp] for sp in self.get_species()])
def reconcile(self, species_tree):
""" Returns the reconcilied topology with the provided species
tree, and a list of evolutionary events inferred from such
reconciliation. """
return get_reconciled_tree(self, species_tree, [])
def get_my_evol_events(self, sos_thr=0.0):
""" Returns a list of duplication and speciation events in
which the current node has been involved. Scanned nodes are
also labeled internally as dup=True|False. You can access this
labels using the 'node.dup' sintaxis.
Method: the algorithm scans all nodes from the given leafName to
the root. Nodes are assumed to be duplications when a species
overlap is found between its child linages. Method is described
more detail in:
"The Human Phylome." Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon
T. Genome Biol. 2007;8(6):R109.
"""
return spoverlap.get_evol_events_from_leaf(self, sos_thr=sos_thr)
def get_descendant_evol_events(self, sos_thr=0.0):
""" Returns a list of **all** duplication and speciation
events detected after this node. Nodes are assumed to be
duplications when a species overlap is found between its child
linages. Method is described more detail in:
"The Human Phylome." Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldon
T. Genome Biol. 2007;8(6):R109.
"""
return spoverlap.get_evol_events_from_root(self, sos_thr=sos_thr)
def get_farthest_oldest_leaf(self, species2age, is_leaf_fn=None):
""" Returns the farthest oldest leaf to the current
one. It requires an species2age dictionary with the age
estimation for all species.
:argument None is_leaf_fn: A pointer to a function that
receives a node instance as unique argument and returns True
or False. It can be used to dynamically collapse nodes, so
they are seen as leaves.
"""
root = self.get_tree_root()
outgroup_dist = 0
outgroup_node = self
outgroup_age = 0 # self.get_age(species2age)
for leaf in root.iter_leaves(is_leaf_fn=is_leaf_fn):
if leaf.get_
|
(newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0, **kargs)
|
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] |
720,904
|
ete3.phylo.phylotree
|
__init__
| null |
def __init__(self, newick=None, alignment=None, alg_format="fasta", \
sp_naming_function=_parse_species, format=0, **kargs):
# _update names?
self._name = "NoName"
self._species = "Unknown"
self._speciesFunction = None
# Caution! native __init__ has to be called after setting
# _speciesFunction to None!!
TreeNode.__init__(self, newick=newick, format=format, **kargs)
# This will be only executed after reading the whole tree,
# because the argument 'alignment' is not passed to the
# PhyloNode constructor during parsing
if alignment:
self.link_to_alignment(alignment, alg_format)
if newick:
self.set_species_naming_function(sp_naming_function)
|
(self, newick=None, alignment=None, alg_format='fasta', sp_naming_function=<function _parse_species at 0x7ff39bbdf760>, format=0, **kargs)
|
[
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] |
721,122
|
ete3.phyloxml
|
Phyloxml
| null |
class Phyloxml(_phyloxml.Phyloxml):
def __repr__(self):
return "PhyloXML project <%s>" %hex(hash(self))
def __init__(self, *args, **kargs):
_phyloxml.Phyloxml.__init__(self, *args, **kargs)
def build_from_file(self, fname):
doc = _phyloxml.parsexml_(fname)
rootNode = doc.getroot()
rootTag, rootClass = _phyloxml.get_root_tag(rootNode)
if rootClass is None:
rootTag = 'phyloxml'
rootClass = self.__class__
self.build(rootNode)
def export(self, outfile=stdout, level=0):
namespace = 'xmlns:phy="http://www.phyloxml.org/1.10/phyloxml.xsd"'
return super(Phyloxml, self).export(outfile=outfile, level=level, namespacedef_=namespace)
|
(*args, **kargs)
|
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] |
721,123
|
ete3.phyloxml
|
__init__
| null |
def __init__(self, *args, **kargs):
_phyloxml.Phyloxml.__init__(self, *args, **kargs)
|
(self, *args, **kargs)
|
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721,124
|
ete3.phyloxml
|
__repr__
| null |
def __repr__(self):
return "PhyloXML project <%s>" %hex(hash(self))
|
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|
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] |
721,125
|
ete3.phyloxml._phyloxml
|
add_phylogeny
| null |
def add_phylogeny(self, value): self.phylogeny.append(value)
|
(self, value)
|
[
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] |
721,127
|
ete3.phyloxml._phyloxml
|
buildAttributes
| null |
def buildAttributes(self, node, attrs, already_processed):
pass
|
(self, node, attrs, already_processed)
|
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] |
721,128
|
ete3.phyloxml._phyloxml
|
buildChildren
| null |
def buildChildren(self, child_, node, nodeName_, fromsubclass_=False):
if nodeName_ == 'phylogeny':
obj_ = Phylogeny.factory()
obj_.build(child_)
self.phylogeny.append(obj_)
|
(self, child_, node, nodeName_, fromsubclass_=False)
|
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] |
721,129
|
ete3.phyloxml
|
build_from_file
| null |
def build_from_file(self, fname):
doc = _phyloxml.parsexml_(fname)
rootNode = doc.getroot()
rootTag, rootClass = _phyloxml.get_root_tag(rootNode)
if rootClass is None:
rootTag = 'phyloxml'
rootClass = self.__class__
self.build(rootNode)
|
(self, fname)
|
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] |
721,130
|
ete3.phyloxml
|
export
| null |
def export(self, outfile=stdout, level=0):
namespace = 'xmlns:phy="http://www.phyloxml.org/1.10/phyloxml.xsd"'
return super(Phyloxml, self).export(outfile=outfile, level=level, namespacedef_=namespace)
|
(self, outfile=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, level=0)
|
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] |
721,131
|
ete3.phyloxml._phyloxml
|
exportAttributes
| null |
def exportAttributes(self, outfile, level, already_processed, namespace_='phy:', name_='Phyloxml'):
pass
|
(self, outfile, level, already_processed, namespace_='phy:', name_='Phyloxml')
|
[
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] |
721,132
|
ete3.phyloxml._phyloxml
|
exportChildren
| null |
def exportChildren(self, outfile, level, namespace_='phy:', name_='Phyloxml', fromsubclass_=False):
for phylogeny_ in self.phylogeny:
phylogeny_.export(outfile, level, namespace_, name_='phylogeny')
|
(self, outfile, level, namespace_='phy:', name_='Phyloxml', fromsubclass_=False)
|
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] |
721,133
|
ete3.phyloxml._phyloxml
|
exportLiteral
| null |
def exportLiteral(self, outfile, level, name_='Phyloxml'):
level += 1
self.exportLiteralAttributes(outfile, level, [], name_)
if self.hasContent_():
self.exportLiteralChildren(outfile, level, name_)
|
(self, outfile, level, name_='Phyloxml')
|
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721,134
|
ete3.phyloxml._phyloxml
|
exportLiteralAttributes
| null |
def exportLiteralAttributes(self, outfile, level, already_processed, name_):
pass
|
(self, outfile, level, already_processed, name_)
|
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] |
721,135
|
ete3.phyloxml._phyloxml
|
exportLiteralChildren
| null |
def exportLiteralChildren(self, outfile, level, name_):
showIndent(outfile, level)
outfile.write('phylogeny=[\n')
level += 1
for phylogeny_ in self.phylogeny:
showIndent(outfile, level)
outfile.write('model_.Phylogeny(\n')
phylogeny_.exportLiteral(outfile, level, name_='Phylogeny')
showIndent(outfile, level)
outfile.write('),\n')
level -= 1
showIndent(outfile, level)
outfile.write('],\n')
|
(self, outfile, level, name_)
|
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] |
721,136
|
ete3.phyloxml._phyloxml
|
factory
| null |
def factory(*args_, **kwargs_):
if Phyloxml.subclass:
return Phyloxml.subclass(*args_, **kwargs_)
else:
return Phyloxml(*args_, **kwargs_)
|
(*args_, **kwargs_)
|
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] |
721,158
|
ete3.phyloxml._phyloxml
|
get_phylogeny
| null |
def get_phylogeny(self): return self.phylogeny
|
(self)
|
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721,159
|
ete3.phyloxml._phyloxml
|
hasContent_
| null |
def hasContent_(self):
if (
self.phylogeny
):
return True
else:
return False
|
(self)
|
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] |
721,160
|
ete3.phyloxml._phyloxml
|
insert_phylogeny
| null |
def insert_phylogeny(self, index, value): self.phylogeny[index] = value
|
(self, index, value)
|
[
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] |
721,161
|
ete3.phyloxml._phyloxml
|
set_phylogeny
| null |
def set_phylogeny(self, phylogeny): self.phylogeny = phylogeny
|
(self, phylogeny)
|
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] |
721,162
|
ete3.phyloxml._phyloxml_tree
|
PhyloxmlTree
|
PhyloTree object supporting phyloXML format.
|
class PhyloxmlTree(PhyloTree):
''' PhyloTree object supporting phyloXML format. '''
def __repr__(self):
return "PhyloXML ETE tree <%s>" %hex(hash(self))
def _get_dist(self):
v = self.phyloxml_clade.get_branch_length_attr()
if v is None:
v = self.phyloxml_clade.get_branch_length()
if v is None:
self._set_dist(self._dist)
v = self.phyloxml_clade.get_branch_length_attr()
return float(v)
def _set_dist(self, value):
try:
self.phyloxml_clade.set_branch_length(float(value))
self.phyloxml_clade.set_branch_length_attr(float(value))
except ValueError:
raise
def _get_support(self):
if len(self.phyloxml_clade.confidence) == 0:
_c = Confidence(valueOf_=1.0, type_="branch_support")
self.phyloxml_clade.add_confidence(_c)
return float(self.phyloxml_clade.confidence[0].valueOf_)
def _set_support(self, value):
self._get_support()
self.phyloxml_clade.confidence[0].valueOf_ = float(value)
def _get_name(self):
return self.phyloxml_clade.get_name()
def _set_name(self, value):
try:
self.phyloxml_clade.set_name(value)
except ValueError:
raise
def _get_children(self):
return self.phyloxml_clade.clade
dist = property(fget=_get_dist, fset=_set_dist)
support = property(fget=_get_support, fset=_set_support)
children = property(fget=_get_children)
name = property(fget=_get_name, fset=_set_name)
def __init__(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs):
if not phyloxml_phylogeny:
self.phyloxml_phylogeny = Phylogeny()
else:
self.phyloxml_phylogeny = phyloxml_phylogeny
if not phyloxml_clade:
self.phyloxml_clade = Clade()
self.phyloxml_clade.set_branch_length(0.0)
self.phyloxml_clade.set_name("NoName")
#self.__support = Confidence(valueOf_=1.0, type_="branch_support")
#self.phyloxml_clade.add_confidence(self.__support)
else:
self.phyloxml_clade = phyloxml_clade
super(PhyloxmlTree, self).__init__(**kargs)
def build(self, node):
nodetype = Tag_pattern_.match(node.tag).groups()[-1]
if nodetype == 'phylogeny':
self.phyloxml_phylogeny.buildAttributes(node, node.attrib, [])
elif nodetype == 'clade':
if "branch_length" in node.attrib:
node.attrib["branch_length_attr"] = node.attrib["branch_length"]
self.phyloxml_clade.buildAttributes(node, node.attrib, [])
for child in node:
nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
self.buildChildren(child, node, nodeName_, nodetype=nodetype)
def buildChildren(self, child_, node, nodeName_, fromsubclass=False, nodetype=None):
if nodetype == 'phylogeny':
baseclass = self.phyloxml_phylogeny
if nodeName_ == 'clade':
self.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
elif nodetype == 'clade':
baseclass = self.phyloxml_clade
if nodeName_ == 'clade':
new_node = self.add_child()
new_node.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
def export(self, outfile=sys.stdout, level=0, namespace_='phy:', name_='Phylogeny', namespacedef_=''):
if not self.up:
self.phyloxml_phylogeny.clade = self.phyloxml_clade
self.phyloxml_clade.clade = self.children
self.phyloxml_phylogeny.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
else:
self.phyloxml_clade.clade = self.children
self.phyloxml_clade.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
|
(phyloxml_clade=None, phyloxml_phylogeny=None, **kargs)
|
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] |
721,168
|
ete3.phyloxml._phyloxml_tree
|
__init__
| null |
def __init__(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs):
if not phyloxml_phylogeny:
self.phyloxml_phylogeny = Phylogeny()
else:
self.phyloxml_phylogeny = phyloxml_phylogeny
if not phyloxml_clade:
self.phyloxml_clade = Clade()
self.phyloxml_clade.set_branch_length(0.0)
self.phyloxml_clade.set_name("NoName")
#self.__support = Confidence(valueOf_=1.0, type_="branch_support")
#self.phyloxml_clade.add_confidence(self.__support)
else:
self.phyloxml_clade = phyloxml_clade
super(PhyloxmlTree, self).__init__(**kargs)
|
(self, phyloxml_clade=None, phyloxml_phylogeny=None, **kargs)
|
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721,172
|
ete3.phyloxml._phyloxml_tree
|
__repr__
| null |
def __repr__(self):
return "PhyloXML ETE tree <%s>" %hex(hash(self))
|
(self)
|
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] |
721,176
|
ete3.phyloxml._phyloxml_tree
|
_get_children
| null |
def _get_children(self):
return self.phyloxml_clade.clade
|
(self)
|
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] |
721,177
|
ete3.phyloxml._phyloxml_tree
|
_get_dist
| null |
def _get_dist(self):
v = self.phyloxml_clade.get_branch_length_attr()
if v is None:
v = self.phyloxml_clade.get_branch_length()
if v is None:
self._set_dist(self._dist)
v = self.phyloxml_clade.get_branch_length_attr()
return float(v)
|
(self)
|
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] |
721,180
|
ete3.phyloxml._phyloxml_tree
|
_get_name
| null |
def _get_name(self):
return self.phyloxml_clade.get_name()
|
(self)
|
[
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] |
721,183
|
ete3.phyloxml._phyloxml_tree
|
_get_support
| null |
def _get_support(self):
if len(self.phyloxml_clade.confidence) == 0:
_c = Confidence(valueOf_=1.0, type_="branch_support")
self.phyloxml_clade.add_confidence(_c)
return float(self.phyloxml_clade.confidence[0].valueOf_)
|
(self)
|
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-0.017571475356817245,
0.047914374619722366
] |
721,189
|
ete3.phyloxml._phyloxml_tree
|
_set_dist
| null |
def _set_dist(self, value):
try:
self.phyloxml_clade.set_branch_length(float(value))
self.phyloxml_clade.set_branch_length_attr(float(value))
except ValueError:
raise
|
(self, value)
|
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] |
721,191
|
ete3.phyloxml._phyloxml_tree
|
_set_name
| null |
def _set_name(self, value):
try:
self.phyloxml_clade.set_name(value)
except ValueError:
raise
|
(self, value)
|
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] |
721,194
|
ete3.phyloxml._phyloxml_tree
|
_set_support
| null |
def _set_support(self, value):
self._get_support()
self.phyloxml_clade.confidence[0].valueOf_ = float(value)
|
(self, value)
|
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] |
721,202
|
ete3.phyloxml._phyloxml_tree
|
build
| null |
def build(self, node):
nodetype = Tag_pattern_.match(node.tag).groups()[-1]
if nodetype == 'phylogeny':
self.phyloxml_phylogeny.buildAttributes(node, node.attrib, [])
elif nodetype == 'clade':
if "branch_length" in node.attrib:
node.attrib["branch_length_attr"] = node.attrib["branch_length"]
self.phyloxml_clade.buildAttributes(node, node.attrib, [])
for child in node:
nodeName_ = Tag_pattern_.match(child.tag).groups()[-1]
self.buildChildren(child, node, nodeName_, nodetype=nodetype)
|
(self, node)
|
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] |
721,203
|
ete3.phyloxml._phyloxml_tree
|
buildChildren
| null |
def buildChildren(self, child_, node, nodeName_, fromsubclass=False, nodetype=None):
if nodetype == 'phylogeny':
baseclass = self.phyloxml_phylogeny
if nodeName_ == 'clade':
self.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
elif nodetype == 'clade':
baseclass = self.phyloxml_clade
if nodeName_ == 'clade':
new_node = self.add_child()
new_node.build(child_)
else:
baseclass.buildChildren(child_, node, nodeName_)
|
(self, child_, node, nodeName_, fromsubclass=False, nodetype=None)
|
[
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] |
721,215
|
ete3.phyloxml._phyloxml_tree
|
export
| null |
def export(self, outfile=sys.stdout, level=0, namespace_='phy:', name_='Phylogeny', namespacedef_=''):
if not self.up:
self.phyloxml_phylogeny.clade = self.phyloxml_clade
self.phyloxml_clade.clade = self.children
self.phyloxml_phylogeny.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
else:
self.phyloxml_clade.clade = self.children
self.phyloxml_clade.export(outfile=outfile, level=level, name_=name_, namespacedef_=namespacedef_)
|
(self, outfile=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, level=0, namespace_='phy:', name_='Phylogeny', namespacedef_='')
|
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] |
721,279
|
ete3.coretype.seqgroup
|
SeqGroup
|
SeqGroup class can be used to store a set of sequences (aligned
or not).
:argument sequences: Path to the file containing the sequences or,
alternatively, the text string containing the same
information.
:argument fasta format: the format in which sequences are
encoded. Current supported formats are: ``fasta``, ``phylip``
(phylip sequencial) and ``iphylip`` (phylip
interleaved). Phylip format forces sequence names to a maximum
of 10 chars. To avoid this effect, you can use the relaxed
phylip format: ``phylip_relaxed`` and ``iphylip_relaxed``.
::
msf = ">seq1\nAAAAAAAAAAA\n>seq2\nTTTTTTTTTTTTT\n"
seqs = SeqGroup(msf, format="fasta")
print seqs.get_seq("seq1")
|
class SeqGroup(object):
"""
SeqGroup class can be used to store a set of sequences (aligned
or not).
:argument sequences: Path to the file containing the sequences or,
alternatively, the text string containing the same
information.
:argument fasta format: the format in which sequences are
encoded. Current supported formats are: ``fasta``, ``phylip``
(phylip sequencial) and ``iphylip`` (phylip
interleaved). Phylip format forces sequence names to a maximum
of 10 chars. To avoid this effect, you can use the relaxed
phylip format: ``phylip_relaxed`` and ``iphylip_relaxed``.
::
msf = ">seq1\\nAAAAAAAAAAA\\n>seq2\\nTTTTTTTTTTTTT\\n"
seqs = SeqGroup(msf, format="fasta")
print seqs.get_seq("seq1")
"""
def __len__(self):
return len(self.id2seq)
def __contains__(self, item):
return item in self.name2id
def __str__(self):
return write_fasta(self)
def __iter__(self):
return self.iter_entries()
def __init__(self, sequences=None , format="fasta", fix_duplicates=True, **kwargs):
self.parsers = {
"fasta": [read_fasta, write_fasta, {}],
"phylip": [read_phylip, write_phylip, {"interleaved":False, "relaxed":False}],
"iphylip": [read_phylip, write_phylip, {"interleaved":True, "relaxed":False}],
"phylip_relaxed": [read_phylip, write_phylip, {"interleaved":False, "relaxed":True}],
"iphylip_relaxed": [read_phylip, write_phylip, {"interleaved":True, "relaxed":True}],
"paml" : [read_paml , write_paml , kwargs ]
}
self.id2name = {}
self.name2id = {}
self.id2comment= {}
self.id2seq = {}
if sequences is not None:
format = format.lower()
if format in self.parsers:
read = self.parsers[format][0]
args = self.parsers[format][2]
read(sequences, obj=self, fix_duplicates=fix_duplicates, **args)
else:
raise ValueError("Unsupported format: [%s]" %format)
def __repr__(self):
return "SeqGroup (%s)" %hex(self.__hash__())
def write(self, format="fasta", outfile=None):
""" Returns the text representation of the sequences in the
supplied given format (default=FASTA). If "oufile" argument is
used, the result is written into the given path."""
format = format.lower()
if format in self.parsers:
write = self.parsers[format][1]
args = self.parsers[format][2]
return write(self, outfile, **args)
else:
raise ValueError("Unsupported format: [%s]" %format)
def iter_entries(self):
""" Returns an iterator over all sequences in the
collection. Each item is a tuple with the sequence name,
sequence, and sequence comments """
for i, seq in six.iteritems(self.id2seq):
yield self.id2name[i], seq, self.id2comment.get(i, [])
def get_seq(self, name):
""" Returns the sequence associated to a given entry name."""
return self.id2seq[self.name2id[name]]
def get_entries(self):
""" Returns the list of entries currently stored."""
keys = list(self.id2seq.keys())
seqs = list(self.id2seq.values())
comments = [self.id2comment.get(x, []) for x in keys]
names = [self.id2name[x] for x in keys]
return list(zip(names, seqs, comments))
def set_seq(self, name, seq, comments = None):
"""Updates or adds a sequence """
if comments is None:
comments = []
name = name.strip()
seq = seq.replace(" ", "")
seq = seq.replace("\t", "")
seq = seq.replace("\n", "")
seq = seq.replace("\r", "")
seqid = self.name2id.get(name, max([0]+list(self.name2id.values()))+1)
self.name2id[name] = seqid
self.id2name[seqid] = name
self.id2comment[seqid] = comments
self.id2seq[seqid] = seq
|
(sequences=None, format='fasta', fix_duplicates=True, **kwargs)
|
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721,280
|
ete3.coretype.seqgroup
|
__contains__
| null |
def __contains__(self, item):
return item in self.name2id
|
(self, item)
|
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0.019481346011161804,
0.002629023278132081,
0.06398524343967438
] |
721,281
|
ete3.coretype.seqgroup
|
__init__
| null |
def __init__(self, sequences=None , format="fasta", fix_duplicates=True, **kwargs):
self.parsers = {
"fasta": [read_fasta, write_fasta, {}],
"phylip": [read_phylip, write_phylip, {"interleaved":False, "relaxed":False}],
"iphylip": [read_phylip, write_phylip, {"interleaved":True, "relaxed":False}],
"phylip_relaxed": [read_phylip, write_phylip, {"interleaved":False, "relaxed":True}],
"iphylip_relaxed": [read_phylip, write_phylip, {"interleaved":True, "relaxed":True}],
"paml" : [read_paml , write_paml , kwargs ]
}
self.id2name = {}
self.name2id = {}
self.id2comment= {}
self.id2seq = {}
if sequences is not None:
format = format.lower()
if format in self.parsers:
read = self.parsers[format][0]
args = self.parsers[format][2]
read(sequences, obj=self, fix_duplicates=fix_duplicates, **args)
else:
raise ValueError("Unsupported format: [%s]" %format)
|
(self, sequences=None, format='fasta', fix_duplicates=True, **kwargs)
|
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721,282
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ete3.coretype.seqgroup
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__iter__
| null |
def __iter__(self):
return self.iter_entries()
|
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721,283
|
ete3.coretype.seqgroup
|
__len__
| null |
def __len__(self):
return len(self.id2seq)
|
(self)
|
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721,284
|
ete3.coretype.seqgroup
|
__repr__
| null |
def __repr__(self):
return "SeqGroup (%s)" %hex(self.__hash__())
|
(self)
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721,285
|
ete3.coretype.seqgroup
|
__str__
| null |
def __str__(self):
return write_fasta(self)
|
(self)
|
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] |
721,286
|
ete3.coretype.seqgroup
|
get_entries
|
Returns the list of entries currently stored.
|
def get_entries(self):
""" Returns the list of entries currently stored."""
keys = list(self.id2seq.keys())
seqs = list(self.id2seq.values())
comments = [self.id2comment.get(x, []) for x in keys]
names = [self.id2name[x] for x in keys]
return list(zip(names, seqs, comments))
|
(self)
|
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] |
721,287
|
ete3.coretype.seqgroup
|
get_seq
|
Returns the sequence associated to a given entry name.
|
def get_seq(self, name):
""" Returns the sequence associated to a given entry name."""
return self.id2seq[self.name2id[name]]
|
(self, name)
|
[
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] |
721,288
|
ete3.coretype.seqgroup
|
iter_entries
|
Returns an iterator over all sequences in the
collection. Each item is a tuple with the sequence name,
sequence, and sequence comments
|
def iter_entries(self):
""" Returns an iterator over all sequences in the
collection. Each item is a tuple with the sequence name,
sequence, and sequence comments """
for i, seq in six.iteritems(self.id2seq):
yield self.id2name[i], seq, self.id2comment.get(i, [])
|
(self)
|
[
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] |
721,289
|
ete3.coretype.seqgroup
|
set_seq
|
Updates or adds a sequence
|
def set_seq(self, name, seq, comments = None):
"""Updates or adds a sequence """
if comments is None:
comments = []
name = name.strip()
seq = seq.replace(" ", "")
seq = seq.replace("\t", "")
seq = seq.replace("\n", "")
seq = seq.replace("\r", "")
seqid = self.name2id.get(name, max([0]+list(self.name2id.values()))+1)
self.name2id[name] = seqid
self.id2name[seqid] = name
self.id2comment[seqid] = comments
self.id2seq[seqid] = seq
|
(self, name, seq, comments=None)
|
[
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] |
721,290
|
ete3.coretype.seqgroup
|
write
|
Returns the text representation of the sequences in the
supplied given format (default=FASTA). If "oufile" argument is
used, the result is written into the given path.
|
def write(self, format="fasta", outfile=None):
""" Returns the text representation of the sequences in the
supplied given format (default=FASTA). If "oufile" argument is
used, the result is written into the given path."""
format = format.lower()
if format in self.parsers:
write = self.parsers[format][1]
args = self.parsers[format][2]
return write(self, outfile, **args)
else:
raise ValueError("Unsupported format: [%s]" %format)
|
(self, format='fasta', outfile=None)
|
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] |
721,291
|
ete3.coretype.tree
|
TreeNode
|
TreeNode (Tree) class is used to store a tree structure. A tree
consists of a collection of TreeNode instances connected in a
hierarchical way. Trees can be loaded from the New Hampshire Newick
format (newick).
:argument newick: Path to the file containing the tree or, alternatively,
the text string containing the same information.
:argument 0 format: subnewick format
.. table::
====== ==============================================
FORMAT DESCRIPTION
====== ==============================================
0 flexible with support values
1 flexible with internal node names
2 all branches + leaf names + internal supports
3 all branches + all names
4 leaf branches + leaf names
5 internal and leaf branches + leaf names
6 internal branches + leaf names
7 leaf branches + all names
8 all names
9 leaf names
100 topology only
====== ==============================================
:returns: a tree node object which represents the base of the tree.
**Examples:**
::
t1 = Tree() # creates an empty tree
t2 = Tree('(A:1,(B:1,(C:1,D:1):0.5):0.5);')
t3 = Tree('/home/user/myNewickFile.txt')
|
class TreeNode(object):
"""
TreeNode (Tree) class is used to store a tree structure. A tree
consists of a collection of TreeNode instances connected in a
hierarchical way. Trees can be loaded from the New Hampshire Newick
format (newick).
:argument newick: Path to the file containing the tree or, alternatively,
the text string containing the same information.
:argument 0 format: subnewick format
.. table::
====== ==============================================
FORMAT DESCRIPTION
====== ==============================================
0 flexible with support values
1 flexible with internal node names
2 all branches + leaf names + internal supports
3 all branches + all names
4 leaf branches + leaf names
5 internal and leaf branches + leaf names
6 internal branches + leaf names
7 leaf branches + all names
8 all names
9 leaf names
100 topology only
====== ==============================================
:returns: a tree node object which represents the base of the tree.
**Examples:**
::
t1 = Tree() # creates an empty tree
t2 = Tree('(A:1,(B:1,(C:1,D:1):0.5):0.5);')
t3 = Tree('/home/user/myNewickFile.txt')
"""
def _get_dist(self):
return self._dist
def _set_dist(self, value):
try:
self._dist = float(value)
except ValueError:
raise TreeError('node dist must be a float number')
def _get_support(self):
return self._support
def _set_support(self, value):
try:
self._support = float(value)
except ValueError:
raise TreeError('node support must be a float number')
def _get_up(self):
return self._up
def _set_up(self, value):
if type(value) == type(self) or value is None:
self._up = value
else:
raise TreeError("bad node_up type")
def _get_children(self):
return self._children
def _set_children(self, value):
if type(value) == list:
for n in value:
if type(n) != type(self):
raise TreeError("Incorrect child node type")
self._children = value
else:
raise TreeError("Incorrect children type")
def _get_style(self):
if self._img_style is None:
self._set_style(None)
return self._img_style
def _set_style(self, value):
self.set_style(value)
#: Branch length distance to parent node. Default = 0.0
img_style = property(fget=_get_style, fset=_set_style)
#: Branch length distance to parent node. Default = 0.0
dist = property(fget=_get_dist, fset=_set_dist)
#: Branch support for current node
support = property(fget=_get_support, fset=_set_support)
#: Pointer to parent node
up = property(fget=_get_up, fset=_set_up)
#: A list of children nodes
children = property(fget=_get_children, fset=_set_children)
def _set_face_areas(self, value):
if isinstance(value, _FaceAreas):
self._faces = value
else:
raise ValueError("[%s] is not a valid FaceAreas instance" %type(value))
def _get_face_areas(self):
if not hasattr(self, "_faces"):
self._faces = _FaceAreas()
return self._faces
faces = property(fget=_get_face_areas, \
fset=_set_face_areas)
def __init__(self, newick=None, format=0, dist=None, support=None,
name=None, quoted_node_names=False):
self._children = []
self._up = None
self._dist = DEFAULT_DIST
self._support = DEFAULT_SUPPORT
self._img_style = None
self.features = set([])
# Add basic features
self.features.update(["dist", "support", "name"])
if dist is not None:
self.dist = dist
if support is not None:
self.support = support
self.name = name if name is not None else DEFAULT_NAME
# Initialize tree
if newick is not None:
self._dist = 0.0
read_newick(newick, root_node = self, format=format,
quoted_names=quoted_node_names)
def __nonzero__(self):
return True
def __bool__(self):
"""
Python3's equivalent of __nonzero__
If this is not defined bool(class_instance) will call
__len__ in python3
"""
return True
def __repr__(self):
return "Tree node '%s' (%s)" %(self.name, hex(self.__hash__()))
def __and__(self, value):
""" This allows to execute tree&'A' to obtain the descendant node
whose name is A"""
value=str(value)
try:
first_match = next(self.iter_search_nodes(name=value))
return first_match
except StopIteration:
raise TreeError("Node not found")
def __add__(self, value):
""" This allows to sum two trees."""
# Should a make the sum with two copies of the original trees?
if type(value) == self.__class__:
new_root = self.__class__()
new_root.add_child(self)
new_root.add_child(value)
return new_root
else:
raise TreeError("Invalid node type")
def __str__(self):
""" Print tree in newick format. """
return self.get_ascii(compact=DEFAULT_COMPACT, \
show_internal=DEFAULT_SHOWINTERNAL)
def __contains__(self, item):
""" Check if item belongs to this node. The 'item' argument must
be a node instance or its associated name."""
if isinstance(item, self.__class__):
return item in set(self.get_descendants())
elif type(item)==str:
return item in set([n.name for n in self.traverse()])
def __len__(self):
"""Node len returns number of children."""
return len(self.get_leaves())
def __iter__(self):
""" Iterator over leaf nodes"""
return self.iter_leaves()
def add_feature(self, pr_name, pr_value):
"""
Add or update a node's feature.
"""
setattr(self, pr_name, pr_value)
self.features.add(pr_name)
def add_features(self, **features):
"""
Add or update several features. """
for fname, fvalue in six.iteritems(features):
setattr(self, fname, fvalue)
self.features.add(fname)
def del_feature(self, pr_name):
"""
Permanently deletes a node's feature.
"""
if hasattr(self, pr_name):
delattr(self, pr_name)
self.features.remove(pr_name)
# Topology management
def add_child(self, child=None, name=None, dist=None, support=None):
"""
Adds a new child to this node. If child node is not suplied
as an argument, a new node instance will be created.
:argument None child: the node instance to be added as a child.
:argument None name: the name that will be given to the child.
:argument None dist: the distance from the node to the child.
:argument None support: the support value of child partition.
:returns: The child node instance
"""
if child is None:
child = self.__class__()
if name is not None:
child.name = name
if dist is not None:
child.dist = dist
if support is not None:
child.support = support
self.children.append(child)
child.up = self
return child
def remove_child(self, child):
"""
Removes a child from this node (parent and child
nodes still exit but are no longer connected).
"""
try:
self.children.remove(child)
except ValueError as e:
raise TreeError("child not found")
else:
child.up = None
re
|
(newick=None, format=0, dist=None, support=None, name=None, quoted_node_names=False)
|
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] |
721,296
|
ete3.coretype.tree
|
__init__
| null |
def __init__(self, newick=None, format=0, dist=None, support=None,
name=None, quoted_node_names=False):
self._children = []
self._up = None
self._dist = DEFAULT_DIST
self._support = DEFAULT_SUPPORT
self._img_style = None
self.features = set([])
# Add basic features
self.features.update(["dist", "support", "name"])
if dist is not None:
self.dist = dist
if support is not None:
self.support = support
self.name = name if name is not None else DEFAULT_NAME
# Initialize tree
if newick is not None:
self._dist = 0.0
read_newick(newick, root_node = self, format=format,
quoted_names=quoted_node_names)
|
(self, newick=None, format=0, dist=None, support=None, name=None, quoted_node_names=False)
|
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721,300
|
ete3.coretype.tree
|
__repr__
| null |
def __repr__(self):
return "Tree node '%s' (%s)" %(self.name, hex(self.__hash__()))
|
(self)
|
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] |
721,477
|
ete3.webplugin.webapp
|
WebTreeApplication
|
Provides a basic WSGI application object which can handle ETE
tree visualization and interactions. Please, see the
webplugin example provided with the ETE installation package
(http://pypi.python.org/pypi/ete3).
|
class WebTreeApplication(object):
""" Provides a basic WSGI application object which can handle ETE
tree visualization and interactions. Please, see the
webplugin example provided with the ETE installation package
(http://pypi.python.org/pypi/ete3)."""
def __init__(self):
# Redirects normal output msgs to stderr, since stdout in web
# application is for the browser
sys.stdout = sys.stderr
self.TreeConstructor = None
self.NODE_TARGET_ACTIONS = ["node", "face"]
self.TREE_TARGET_ACTIONS = ["layout", "search"]
self.actions = []
self._layout = None
self._tree_style = None
self._width = None
self._height = None
self._size_units = "px"
self._custom_tree_renderer = None
self._treeid2layout = {}
self._external_app_handler = None
self._treeid2tree = {}
self._treeid2cache = {}
self._treeid2index = {}
self.queries = {}
self.CONFIG = {
"temp_dir":"/var/www/webplugin/",
"temp_url":"http://localhost/webplugin/tmp",
"DISPLAY" :":0" # Used by ete to render images
}
def set_tree_size(self, w, h, units="px"):
""" Fix the size of tree image """
self._width = w
self._height = h
self._size_units = units
def set_external_app_handler(self, handler):
""" Sets a custom function that will extend current WSGI
application."""
self._external_app_handler = handler
def set_external_tree_renderer(self, handler):
""" If the tree needs to be processed every time is going to
be drawn, the task can be delegated. """
self._custom_tree_renderer = handler
def register_action(self, name, target, handler, checker, html_generator):
""" Adds a new web interactive function associated to tree
nodes. """
self.actions.append([name, target, handler, checker, html_generator])
def set_tree_loader(self, TreeConstructor):
""" Delegate tree constructor. It allows to customize the Tree
class used to create new tree instances. """
self._tree = TreeConstructor
def set_default_layout_fn(self, layout_fn):
""" Fix the layout function used to render the tree. """
self._layout = layout_fn
def set_tree_style(self, handler):
""" Fix a :class:`TreeStyle` instance to render tree images. """
self._tree_style = handler
def _get_html_map(self, img_map, treeid, mapid, tree):
# Scans for node-enabled actions.
nid2actions = {}
nid2face_actions = {}
for n in tree.traverse():
for aindex, (action, target, handler, checker, html_generator) in enumerate(self.actions):
if target == "node" and (not checker or checker(n)):
nid2actions.setdefault(int(n._nid), []).append(aindex)
elif target == "face" and (not checker or checker(n)):
nid2face_actions.setdefault(int(n._nid), []).append(aindex)
html_map = '<MAP NAME="%s" class="ete_tree_img">' %(mapid)
if img_map["nodes"]:
for x1, y1, x2, y2, nodeid, text in img_map["nodes"]:
text = "" if not text else text
area = img_map["node_areas"].get(int(nodeid), [0,0,0,0])
html_map += """ <AREA SHAPE="rect" COORDS="%s,%s,%s,%s" onMouseOut='unhighlight_node();' onMouseOver='highlight_node("#%s", "%s", %s, %s, %s, %s);' onClick='show_context_menu("%s", "%s", "%s");' href="javascript:void('%s');">""" %\
(int(x1), int(y1), int(x2), int(y2),
treeid, text, area[0], area[1], area[2]-area[0], area[3]-area[1],
treeid, nodeid, ','.join(map(str, nid2actions.get(nodeid,[]))), str(nodeid) )
if img_map["faces"]:
for x1, y1, x2, y2, nodeid, text in img_map["faces"]:
text = "" if not text else text
area = img_map["node_areas"].get(int(nodeid), [0,0,0,0])
html_map += """ <AREA SHAPE="rect" COORDS="%s,%s,%s,%s" onMouseOut='unhighlight_node(); hide_face_popup();' onMouseOver='highlight_node("#%s", "%s", %s, %s, %s, %s); show_face_popup("%s", "%s", "%s", "%s");' onClick='show_context_menu("%s", "%s", "%s", "%s");' href="javascript:void('%s');">""" %\
(int(x1),int(y1),int(x2),int(y2),
treeid, text, area[0], area[1], area[2]-area[0], area[3]-area[1],
treeid, nodeid, ','.join(map(str, nid2actions.get(nodeid,[])+nid2face_actions.get(nodeid,[]) )), text,
treeid, nodeid, ','.join(map(str, nid2actions.get(nodeid,[])+nid2face_actions.get(nodeid,[]) )), text,
text,
)
html_map += '</MAP>'
return html_map
def _load_tree(self, treeid, tree=None, cache_file=None):
# if a tree is given, it overwrites previous versions
if tree and isinstance(tree, str):
tree = self._tree(tree)
self._treeid2tree[treeid] = tree
self._load_tree_index(treeid)
elif tree:
self._treeid2tree[treeid] = tree
self._load_tree_index(treeid)
self._treeid2cache[treeid] = cache_file if cache_file else "%s.pkl" %treeid
# if no tree is given, and not in memmory, it tries to loaded
# from previous sessions
if treeid not in self._treeid2tree:
self._load_tree_from_path(self._treeid2cache[treeid])
# Returns True if tree and indexes are loaded
return (treeid in self._treeid2tree) and (treeid in self._treeid2index)
def _load_tree_from_path(self, pkl_path):
tree_path = os.path.join(self.CONFIG["temp_dir"], pkl_path)
if os.path.exists(tree_path):
print(six.moves.cPickle.load(open(tree_path)))
t = self._treeid2tree[treeid] = six.moves.cPickle.load(open(tree_path))
self._load_tree_index(treeid)
return True
else:
return False
def _load_tree_index(self, treeid):
if not self._treeid2index.get(treeid, {}):
tree_index = self._treeid2index[treeid] = {}
t = self._treeid2tree[treeid]
for n in t.traverse():
if hasattr(n, "_nid"):
tree_index[str(n._nid)] = n
return True
else:
return False
def _dump_tree_to_file(self, t, treeid):
tree_path = os.path.join(self.CONFIG["temp_dir"], treeid+".pkl")
six.moves.cPickle.dump(t, open(tree_path, "wb"))
#open(tree_path, "w").write(t.write(features=[]))
def _get_tree_img(self, treeid, pre_drawing_action=None):
img_url = os.path.join(self.CONFIG["temp_url"], treeid+".png?"+str(time.time()))
img_path = os.path.join(self.CONFIG["temp_dir"], treeid+".png")
t = self._treeid2tree[treeid]
tree_index = self._treeid2index[treeid]
if pre_drawing_action:
atype, handler, arguments = pre_drawing_action
if atype in set(["node", "face"]) and len(arguments)==1 and handler:
nid = arguments[0]
node = tree_index.get(str(nid), None)
handler(node)
elif atype == "tree":
handler(t, arguments[0])
elif atype == "search":
handler(t, arguments[0])
elif atype == "layout":
self._treeid2layout[treeid] = handler
layout_fn = self._treeid2layout.get(treeid, self._layout)
mapid = "img_map_"+str(time.time())
img_map = _render_tree(t, img_path, self.CONFIG["DISPLAY"], layout = layout_fn,
tree_style = self._tree_style,
w=self._width,
h=self._height,
units=self._size_units)
html_map = self._get_html_map(img_map, treeid, mapid, t)
for n in t.traverse():
self._treeid2index[treeid][str(n._nid)]=n
if hasattr(n, "_Q
|
()
|
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] |
721,478
|
ete3.webplugin.webapp
|
__call__
|
This function is executed when the application is called
by the WSGI apache module. It is, therefore, in charge of
answering web requests.
|
def __call__(self, environ, start_response):
""" This function is executed when the application is called
by the WSGI apache module. It is, therefore, in charge of
answering web requests."""
path = environ['PATH_INFO'].split("/")
start_response('202 OK', [('content-type', 'text/plain')])
if environ['REQUEST_METHOD'].upper() == 'GET' and environ['QUERY_STRING']:
self.queries = cgi.parse_qs(environ['QUERY_STRING'])
elif environ['REQUEST_METHOD'].upper() == 'POST' and environ['wsgi.input']:
self.queries = cgi.parse_qs(environ['wsgi.input'].read())
else:
self.queries = {}
method = path[1]
treeid = self.queries.get("treeid", [None])[0]
nodeid = self.queries.get("nid", [None])[0]
textface = self.queries.get("textface", [None])[0]
actions = self.queries.get("show_actions", [None])[0]
tree = self.queries.get("tree", [None])[0]
search_term = self.queries.get("search_term", [None])[0]
aindex = self.queries.get("aindex", [None])[0]
if method == "draw":
# if not treeid is given, generate one
if not treeid:
treeid = md5(str(time.time())).hexdigest()
if not self._load_tree(treeid, tree):
return "draw: Cannot load the tree: %s" %treeid
if self._custom_tree_renderer:
t = self._treeid2tree[treeid]
return self._custom_tree_renderer(t, treeid, self)
elif t and treeid:
return self._get_tree_img(treeid=treeid)
else:
return "No tree to draw"
elif method == "get_menu":
if not self._load_tree(treeid):
return "get_menu: Cannot load the tree: %s" %treeid
if nodeid:
tree_index = self._treeid2index[treeid]
node = tree_index[nodeid]
else:
node = None
if textface:
header = str(textface).strip()
else:
header = "Menu"
html = """<div id="ete_popup_header"><span id="ete_popup_header_text">%s</span><div id="ete_close_popup" onClick='hide_popup();'></div></div><ul>""" %\
(header)
for i in map(int, actions.split(",")):
aname, target, handler, checker, html_generator = self.actions[i]
if html_generator:
html += html_generator(i, treeid, nodeid, textface, node)
else:
html += """<li><a href='javascript:void(0);' onClick='hide_popup(); run_action("%s", "%s", "%s");'> %s </a></li> """ %\
(treeid, nodeid, i, aname)
html += '</ul>'
return html
elif method == "action":
if not self._load_tree(treeid):
return "action: Cannot load the tree: %s" %treeid
if aindex is None:
# just refresh tree
return self._get_tree_img(treeid=treeid)
else:
aname, target, handler, checker, html_generator = self.actions[int(aindex)]
if target in set(["node", "face", "layout"]):
return self._get_tree_img(treeid=treeid, pre_drawing_action=[target, handler, [nodeid]])
elif target in set(["search"]):
return self._get_tree_img(treeid=treeid, pre_drawing_action=[target, handler, [search_term]])
elif target in set(["refresh"]):
return self._get_tree_img(treeid=treeid)
return "Bad guy"
elif self._external_app_handler:
return self._external_app_handler(environ, start_response, self.queries)
else:
return '\n'.join(map(str, list(environ.items()))) + str(self.queries) + '\t\n'.join(environ['wsgi.input'])
|
(self, environ, start_response)
|
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] |
721,479
|
ete3.webplugin.webapp
|
__init__
| null |
def __init__(self):
# Redirects normal output msgs to stderr, since stdout in web
# application is for the browser
sys.stdout = sys.stderr
self.TreeConstructor = None
self.NODE_TARGET_ACTIONS = ["node", "face"]
self.TREE_TARGET_ACTIONS = ["layout", "search"]
self.actions = []
self._layout = None
self._tree_style = None
self._width = None
self._height = None
self._size_units = "px"
self._custom_tree_renderer = None
self._treeid2layout = {}
self._external_app_handler = None
self._treeid2tree = {}
self._treeid2cache = {}
self._treeid2index = {}
self.queries = {}
self.CONFIG = {
"temp_dir":"/var/www/webplugin/",
"temp_url":"http://localhost/webplugin/tmp",
"DISPLAY" :":0" # Used by ete to render images
}
|
(self)
|
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] |
721,480
|
ete3.webplugin.webapp
|
_dump_tree_to_file
| null |
def _dump_tree_to_file(self, t, treeid):
tree_path = os.path.join(self.CONFIG["temp_dir"], treeid+".pkl")
six.moves.cPickle.dump(t, open(tree_path, "wb"))
#open(tree_path, "w").write(t.write(features=[]))
|
(self, t, treeid)
|
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] |
721,481
|
ete3.webplugin.webapp
|
_get_html_map
| null |
def _get_html_map(self, img_map, treeid, mapid, tree):
# Scans for node-enabled actions.
nid2actions = {}
nid2face_actions = {}
for n in tree.traverse():
for aindex, (action, target, handler, checker, html_generator) in enumerate(self.actions):
if target == "node" and (not checker or checker(n)):
nid2actions.setdefault(int(n._nid), []).append(aindex)
elif target == "face" and (not checker or checker(n)):
nid2face_actions.setdefault(int(n._nid), []).append(aindex)
html_map = '<MAP NAME="%s" class="ete_tree_img">' %(mapid)
if img_map["nodes"]:
for x1, y1, x2, y2, nodeid, text in img_map["nodes"]:
text = "" if not text else text
area = img_map["node_areas"].get(int(nodeid), [0,0,0,0])
html_map += """ <AREA SHAPE="rect" COORDS="%s,%s,%s,%s" onMouseOut='unhighlight_node();' onMouseOver='highlight_node("#%s", "%s", %s, %s, %s, %s);' onClick='show_context_menu("%s", "%s", "%s");' href="javascript:void('%s');">""" %\
(int(x1), int(y1), int(x2), int(y2),
treeid, text, area[0], area[1], area[2]-area[0], area[3]-area[1],
treeid, nodeid, ','.join(map(str, nid2actions.get(nodeid,[]))), str(nodeid) )
if img_map["faces"]:
for x1, y1, x2, y2, nodeid, text in img_map["faces"]:
text = "" if not text else text
area = img_map["node_areas"].get(int(nodeid), [0,0,0,0])
html_map += """ <AREA SHAPE="rect" COORDS="%s,%s,%s,%s" onMouseOut='unhighlight_node(); hide_face_popup();' onMouseOver='highlight_node("#%s", "%s", %s, %s, %s, %s); show_face_popup("%s", "%s", "%s", "%s");' onClick='show_context_menu("%s", "%s", "%s", "%s");' href="javascript:void('%s');">""" %\
(int(x1),int(y1),int(x2),int(y2),
treeid, text, area[0], area[1], area[2]-area[0], area[3]-area[1],
treeid, nodeid, ','.join(map(str, nid2actions.get(nodeid,[])+nid2face_actions.get(nodeid,[]) )), text,
treeid, nodeid, ','.join(map(str, nid2actions.get(nodeid,[])+nid2face_actions.get(nodeid,[]) )), text,
text,
)
html_map += '</MAP>'
return html_map
|
(self, img_map, treeid, mapid, tree)
|
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] |
721,482
|
ete3.webplugin.webapp
|
_get_tree_img
| null |
def _get_tree_img(self, treeid, pre_drawing_action=None):
img_url = os.path.join(self.CONFIG["temp_url"], treeid+".png?"+str(time.time()))
img_path = os.path.join(self.CONFIG["temp_dir"], treeid+".png")
t = self._treeid2tree[treeid]
tree_index = self._treeid2index[treeid]
if pre_drawing_action:
atype, handler, arguments = pre_drawing_action
if atype in set(["node", "face"]) and len(arguments)==1 and handler:
nid = arguments[0]
node = tree_index.get(str(nid), None)
handler(node)
elif atype == "tree":
handler(t, arguments[0])
elif atype == "search":
handler(t, arguments[0])
elif atype == "layout":
self._treeid2layout[treeid] = handler
layout_fn = self._treeid2layout.get(treeid, self._layout)
mapid = "img_map_"+str(time.time())
img_map = _render_tree(t, img_path, self.CONFIG["DISPLAY"], layout = layout_fn,
tree_style = self._tree_style,
w=self._width,
h=self._height,
units=self._size_units)
html_map = self._get_html_map(img_map, treeid, mapid, t)
for n in t.traverse():
self._treeid2index[treeid][str(n._nid)]=n
if hasattr(n, "_QtItem_"):
n._QtItem_ = None
delattr(n, "_QtItem_")
tree_actions = []
for aindex, (action, target, handler, checker, html_generator) in enumerate(self.actions):
if target in self.TREE_TARGET_ACTIONS and (not checker or checker(t)):
tree_actions.append(aindex)
try:
version_tag = __version__
except NameError:
version_tag = "ete3"
self._dump_tree_to_file(t, treeid)
ete_publi = '<div style="margin:0px;padding:0px;text-align:left;"><a href="http://etetoolkit.org" style="font-size:7pt;" target="_blank" >%s</a></div>' %\
(version_tag)
img_html = """<img id="%s" class="ete_tree_img" src="%s" USEMAP="#%s" onLoad='javascript:bind_popup();' onclick='javascript:show_context_menu("%s", "", "%s");' >""" %\
(treeid, img_url, mapid, treeid, ','.join(map(str, tree_actions)))
tree_div_id = "ETE_tree_"+str(treeid)
return html_map+ '<div id="%s" >'%tree_div_id + img_html + ete_publi + "</div>"
|
(self, treeid, pre_drawing_action=None)
|
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] |
721,483
|
ete3.webplugin.webapp
|
_load_tree
| null |
def _load_tree(self, treeid, tree=None, cache_file=None):
# if a tree is given, it overwrites previous versions
if tree and isinstance(tree, str):
tree = self._tree(tree)
self._treeid2tree[treeid] = tree
self._load_tree_index(treeid)
elif tree:
self._treeid2tree[treeid] = tree
self._load_tree_index(treeid)
self._treeid2cache[treeid] = cache_file if cache_file else "%s.pkl" %treeid
# if no tree is given, and not in memmory, it tries to loaded
# from previous sessions
if treeid not in self._treeid2tree:
self._load_tree_from_path(self._treeid2cache[treeid])
# Returns True if tree and indexes are loaded
return (treeid in self._treeid2tree) and (treeid in self._treeid2index)
|
(self, treeid, tree=None, cache_file=None)
|
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] |
721,484
|
ete3.webplugin.webapp
|
_load_tree_from_path
| null |
def _load_tree_from_path(self, pkl_path):
tree_path = os.path.join(self.CONFIG["temp_dir"], pkl_path)
if os.path.exists(tree_path):
print(six.moves.cPickle.load(open(tree_path)))
t = self._treeid2tree[treeid] = six.moves.cPickle.load(open(tree_path))
self._load_tree_index(treeid)
return True
else:
return False
|
(self, pkl_path)
|
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] |
721,485
|
ete3.webplugin.webapp
|
_load_tree_index
| null |
def _load_tree_index(self, treeid):
if not self._treeid2index.get(treeid, {}):
tree_index = self._treeid2index[treeid] = {}
t = self._treeid2tree[treeid]
for n in t.traverse():
if hasattr(n, "_nid"):
tree_index[str(n._nid)] = n
return True
else:
return False
|
(self, treeid)
|
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] |
721,486
|
ete3.webplugin.webapp
|
register_action
|
Adds a new web interactive function associated to tree
nodes.
|
def register_action(self, name, target, handler, checker, html_generator):
""" Adds a new web interactive function associated to tree
nodes. """
self.actions.append([name, target, handler, checker, html_generator])
|
(self, name, target, handler, checker, html_generator)
|
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] |
721,487
|
ete3.webplugin.webapp
|
set_default_layout_fn
|
Fix the layout function used to render the tree.
|
def set_default_layout_fn(self, layout_fn):
""" Fix the layout function used to render the tree. """
self._layout = layout_fn
|
(self, layout_fn)
|
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] |
721,488
|
ete3.webplugin.webapp
|
set_external_app_handler
|
Sets a custom function that will extend current WSGI
application.
|
def set_external_app_handler(self, handler):
""" Sets a custom function that will extend current WSGI
application."""
self._external_app_handler = handler
|
(self, handler)
|
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] |
721,489
|
ete3.webplugin.webapp
|
set_external_tree_renderer
|
If the tree needs to be processed every time is going to
be drawn, the task can be delegated.
|
def set_external_tree_renderer(self, handler):
""" If the tree needs to be processed every time is going to
be drawn, the task can be delegated. """
self._custom_tree_renderer = handler
|
(self, handler)
|
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-0.052694354206323624,
0.10327433049678802,
0.0505799725651741,
0.022580934688448906,
0.03974376618862152
] |
721,490
|
ete3.webplugin.webapp
|
set_tree_loader
|
Delegate tree constructor. It allows to customize the Tree
class used to create new tree instances.
|
def set_tree_loader(self, TreeConstructor):
""" Delegate tree constructor. It allows to customize the Tree
class used to create new tree instances. """
self._tree = TreeConstructor
|
(self, TreeConstructor)
|
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] |
721,491
|
ete3.webplugin.webapp
|
set_tree_size
|
Fix the size of tree image
|
def set_tree_size(self, w, h, units="px"):
""" Fix the size of tree image """
self._width = w
self._height = h
self._size_units = units
|
(self, w, h, units='px')
|
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] |
721,492
|
ete3.webplugin.webapp
|
set_tree_style
|
Fix a :class:`TreeStyle` instance to render tree images.
|
def set_tree_style(self, handler):
""" Fix a :class:`TreeStyle` instance to render tree images. """
self._tree_style = handler
|
(self, handler)
|
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] |
721,497
|
ete3.ncbi_taxonomy.ncbiquery
|
is_taxadb_up_to_date
|
Check if a valid and up-to-date taxa.sqlite database exists
If dbfile= is not specified, DEFAULT_TAXADB is assumed
|
def is_taxadb_up_to_date(dbfile=DEFAULT_TAXADB):
"""Check if a valid and up-to-date taxa.sqlite database exists
If dbfile= is not specified, DEFAULT_TAXADB is assumed
"""
db = sqlite3.connect(dbfile)
try:
r = db.execute('SELECT version FROM stats;')
version = r.fetchone()[0]
except (sqlite3.OperationalError, ValueError, IndexError, TypeError):
version = None
db.close()
if version != DB_VERSION:
return False
return True
|
(dbfile='/root/.etetoolkit/taxa.sqlite')
|
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] |
721,515
|
pydal.base
|
DAL
|
An instance of this class represents a database connection
Args:
uri(str): contains information for connecting to a database.
Defaults to `'sqlite://dummy.db'`
Note:
experimental: you can specify a dictionary as uri
parameter i.e. with::
db = DAL({"uri": "sqlite://storage.sqlite",
"tables": {...}, ...})
for an example of dict input you can check the output
of the scaffolding db model with
db.as_dict()
Note that for compatibility with Python older than
version 2.6.5 you should cast your dict input keys
to str due to a syntax limitation on kwarg names.
for proper DAL dictionary input you can use one of::
obj = serializers.cast_keys(dict, [encoding="utf-8"])
#or else (for parsing json input)
obj = serializers.loads_json(data, unicode_keys=False)
pool_size: How many open connections to make to the database object.
folder: where .table files will be created. Automatically set within
web2py. Use an explicit path when using DAL outside web2py
db_codec: string encoding of the database (default: 'UTF-8')
table_hash: database identifier with .tables. If your connection hash
change you can still using old .tables if they have
table_hash as prefix
check_reserved: list of adapters to check tablenames and column names
against sql/nosql reserved keywords. Defaults to `None`
- 'common' List of sql keywords that are common to all database
types such as "SELECT, INSERT". (recommended)
- 'all' Checks against all known SQL keywords
- '<adaptername>'' Checks against the specific adapters list of
keywords
- '<adaptername>_nonreserved' Checks against the specific adapters
list of nonreserved keywords. (if available)
migrate: sets default migrate behavior for all tables
fake_migrate: sets default fake_migrate behavior for all tables
migrate_enabled: If set to False disables ALL migrations
fake_migrate_all: If set to True fake migrates ALL tables
attempts: Number of times to attempt connecting
auto_import: If set to True, tries import automatically table
definitions from the databases folder (works only for simple models)
bigint_id: If set, turn on bigint instead of int for id and reference
fields
lazy_tables: delays table definition until table access
after_connection: can a callable that will be executed after the
connection
Example:
Use as::
db = DAL('sqlite://test.db')
or::
db = DAL(**{"uri": ..., "tables": [...]...}) # experimental
db.define_table('tablename', Field('fieldname1'),
Field('fieldname2'))
|
class DAL(with_metaclass(MetaDAL, Serializable, BasicStorage)):
"""
An instance of this class represents a database connection
Args:
uri(str): contains information for connecting to a database.
Defaults to `'sqlite://dummy.db'`
Note:
experimental: you can specify a dictionary as uri
parameter i.e. with::
db = DAL({"uri": "sqlite://storage.sqlite",
"tables": {...}, ...})
for an example of dict input you can check the output
of the scaffolding db model with
db.as_dict()
Note that for compatibility with Python older than
version 2.6.5 you should cast your dict input keys
to str due to a syntax limitation on kwarg names.
for proper DAL dictionary input you can use one of::
obj = serializers.cast_keys(dict, [encoding="utf-8"])
#or else (for parsing json input)
obj = serializers.loads_json(data, unicode_keys=False)
pool_size: How many open connections to make to the database object.
folder: where .table files will be created. Automatically set within
web2py. Use an explicit path when using DAL outside web2py
db_codec: string encoding of the database (default: 'UTF-8')
table_hash: database identifier with .tables. If your connection hash
change you can still using old .tables if they have
table_hash as prefix
check_reserved: list of adapters to check tablenames and column names
against sql/nosql reserved keywords. Defaults to `None`
- 'common' List of sql keywords that are common to all database
types such as "SELECT, INSERT". (recommended)
- 'all' Checks against all known SQL keywords
- '<adaptername>'' Checks against the specific adapters list of
keywords
- '<adaptername>_nonreserved' Checks against the specific adapters
list of nonreserved keywords. (if available)
migrate: sets default migrate behavior for all tables
fake_migrate: sets default fake_migrate behavior for all tables
migrate_enabled: If set to False disables ALL migrations
fake_migrate_all: If set to True fake migrates ALL tables
attempts: Number of times to attempt connecting
auto_import: If set to True, tries import automatically table
definitions from the databases folder (works only for simple models)
bigint_id: If set, turn on bigint instead of int for id and reference
fields
lazy_tables: delays table definition until table access
after_connection: can a callable that will be executed after the
connection
Example:
Use as::
db = DAL('sqlite://test.db')
or::
db = DAL(**{"uri": ..., "tables": [...]...}) # experimental
db.define_table('tablename', Field('fieldname1'),
Field('fieldname2'))
"""
serializers = None
validators = None
representers = {}
validators_method = default_validators
uuid = staticmethod(uuidstr)
logger = logging.getLogger("pyDAL")
Field = Field
Table = Table
Rows = Rows
Row = Row
record_operators = {"update_record": RecordUpdater, "delete_record": RecordDeleter}
execution_handlers = [TimingHandler]
def __new__(cls, uri="sqlite://dummy.db", *args, **kwargs):
if not hasattr(THREAD_LOCAL, "_pydal_db_instances_"):
THREAD_LOCAL._pydal_db_instances_ = {}
if not hasattr(THREAD_LOCAL, "_pydal_db_instances_zombie_"):
THREAD_LOCAL._pydal_db_instances_zombie_ = {}
if uri == "<zombie>":
db_uid = kwargs["db_uid"] # a zombie must have a db_uid!
if db_uid in THREAD_LOCAL._pydal_db_instances_:
db_group = THREAD_LOCAL._pydal_db_instances_[db_uid]
db = db_group[-1]
elif db_uid in THREAD_LOCAL._pydal_db_instances_zombie_:
db = THREAD_LOCAL._pydal_db_instances_zombie_[db_uid]
else:
db = super(DAL, cls).__new__(cls)
THREAD_LOCAL._pydal_db_instances_zombie_[db_uid] = db
else:
db_uid = kwargs.get("db_uid", hashlib_md5(repr(uri)).hexdigest())
if db_uid in THREAD_LOCAL._pydal_db_instances_zombie_:
db = THREAD_LOCAL._pydal_db_instances_zombie_[db_uid]
del THREAD_LOCAL._pydal_db_instances_zombie_[db_uid]
else:
db = super(DAL, cls).__new__(cls)
db_group = THREAD_LOCAL._pydal_db_instances_.get(db_uid, [])
db_group.append(db)
THREAD_LOCAL._pydal_db_instances_[db_uid] = db_group
db._db_uid = db_uid
return db
@staticmethod
def set_folder(folder):
# ## this allows gluon to set a folder for this thread
# ## <<<<<<<<< Should go away as new DAL replaces old sql.py
BaseAdapter.set_folder(folder)
@staticmethod
def get_instances():
"""
Returns a dictionary with uri as key with timings and defined tables::
{'sqlite://storage.sqlite': {
'dbstats': [(select auth_user.email from auth_user, 0.02009)],
'dbtables': {
'defined': ['auth_cas', 'auth_event', 'auth_group',
'auth_membership', 'auth_permission', 'auth_user'],
'lazy': '[]'
}
}
}
"""
dbs = getattr(THREAD_LOCAL, "_pydal_db_instances_", {}).items()
infos = {}
for db_uid, db_group in dbs:
for db in db_group:
if not db._uri:
continue
k = hide_password(db._adapter.uri)
infos[k] = dict(
dbstats=[(row[0], row[1]) for row in db._timings],
dbtables={
"defined": sorted(
list(set(db.tables) - set(db._LAZY_TABLES.keys()))
),
"lazy": sorted(db._LAZY_TABLES.keys()),
},
)
return infos
@staticmethod
def distributed_transaction_begin(*instances):
if not instances:
return
thread_key = "%s.%s" % (socket.gethostname(), threading.current_thread())
instances = enumerate(instances)
keys = ["%s.%i" % (thread_key, i) for (i, db) in instances]
for i, db in instances:
if not db._adapter.support_distributed_transaction():
raise SyntaxError(
"distributed transaction not suported by %s" % db._dbname
)
for i, db in instances:
db._adapter.distributed_transaction_begin(keys[i])
@staticmethod
def distributed_transaction_commit(*instances):
if not instances:
return
instances = enumerate(instances)
thread_key = "%s.%s" % (socket.gethostname(), threading.current_thread())
keys = ["%s.%i" % (thread_key, i) for (i, db) in instances]
for i, db in instances:
if not db._adapter.support_distributed_transaction():
raise SyntaxError(
"distributed transaction not suported by %s" % db._dbanme
)
try:
for i, db in instances:
db._adapter.prepare(keys[i])
except:
for i, db in instances:
db._adapter.rollback_prepared(keys[i])
raise RuntimeError("failure to commit distributed transaction")
else:
for i, db in instances:
db._adapter.commit_prepared(keys[i])
return
def __init__(
self,
uri="sqlite://dummy.db",
pool_size=0,
folder=None,
db_codec="UTF-8",
check_reserved=None,
m
|
(*args, **kwargs)
|
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] |
721,517
|
pydal.base
|
__call__
| null |
def __call__(self, query=None, ignore_common_filters=None):
return self.where(query, ignore_common_filters)
|
(self, query=None, ignore_common_filters=None)
|
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721,521
|
pydal.base
|
__getitem__
| null |
def __getitem__(self, key):
return self.__getattr__(str(key))
|
(self, key)
|
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] |
721,522
|
pydal.base
|
__init__
| null |
def __init__(
self,
uri="sqlite://dummy.db",
pool_size=0,
folder=None,
db_codec="UTF-8",
check_reserved=None,
migrate=True,
fake_migrate=False,
migrate_enabled=True,
fake_migrate_all=False,
decode_credentials=False,
driver_args=None,
adapter_args=None,
attempts=5,
auto_import=False,
bigint_id=False,
debug=False,
lazy_tables=False,
db_uid=None,
after_connection=None,
tables=None,
ignore_field_case=True,
entity_quoting=True,
table_hash=None,
):
if uri == "<zombie>" and db_uid is not None:
return
super(DAL, self).__init__()
if not issubclass(self.Rows, Rows):
raise RuntimeError("`Rows` class must be a subclass of pydal.objects.Rows")
if not issubclass(self.Row, Row):
raise RuntimeError("`Row` class must be a subclass of pydal.objects.Row")
from .drivers import DRIVERS, is_jdbc
self._drivers_available = DRIVERS
if not decode_credentials:
credential_decoder = lambda cred: cred
else:
credential_decoder = lambda cred: unquote(cred)
self._folder = folder
if folder:
self.set_folder(folder)
self._uri = uri
self._pool_size = pool_size
self._db_codec = db_codec
self._pending_references = {}
self._request_tenant = "request_tenant"
self._common_fields = []
self._referee_name = "%(table)s"
self._bigint_id = bigint_id
self._debug = debug
self._migrated = []
self._LAZY_TABLES = {}
self._lazy_tables = lazy_tables
self._tables = SQLCallableList()
self._aliased_tables = threading.local()
self._driver_args = driver_args
self._adapter_args = adapter_args
self._check_reserved = check_reserved
self._decode_credentials = decode_credentials
self._attempts = attempts
self._ignore_field_case = ignore_field_case
if not str(attempts).isdigit() or attempts < 0:
attempts = 5
if uri:
uris = isinstance(uri, (list, tuple)) and uri or [uri]
connected = False
for k in range(attempts):
for uri in uris:
try:
from .adapters import adapters
if is_jdbc and not uri.startswith("jdbc:"):
uri = "jdbc:" + uri
self._dbname = REGEX_DBNAME.match(uri).group()
# notice that driver args or {} else driver_args
# defaults to {} global, not correct
kwargs = dict(
db=self,
uri=uri,
pool_size=pool_size,
folder=folder,
db_codec=db_codec,
credential_decoder=credential_decoder,
driver_args=driver_args or {},
adapter_args=adapter_args or {},
after_connection=after_connection,
entity_quoting=entity_quoting,
)
adapter = adapters.get_for(self._dbname)
self._adapter = adapter(**kwargs)
# self._adapter.ignore_field_case = ignore_field_case
if bigint_id:
self._adapter.dialect._force_bigints()
# if there are multiple URIs to try in sequence, do not defer connection
if len(uris) > 1:
self._adapter.connector()
connected = True
break
except SyntaxError:
raise
except Exception:
tb = traceback.format_exc()
self.logger.debug(
"DEBUG: connect attempt %i, connection error:\n%s" % (k, tb)
)
if connected:
break
else:
time.sleep(1)
if not connected:
raise RuntimeError(
"Failure to connect, tried %d times:\n%s" % (attempts, tb)
)
else:
self._adapter = NullAdapter(
db=self,
pool_size=0,
uri="None",
folder=folder,
db_codec=db_codec,
after_connection=after_connection,
entity_quoting=entity_quoting,
)
migrate = fake_migrate = False
self.validators_method = None
self.validators = None
adapter = self._adapter
self._uri_hash = table_hash or hashlib_md5(adapter.uri).hexdigest()
if check_reserved:
from .contrib.reserved_sql_keywords import ADAPTERS as RSK
self.RSK = RSK
self._migrate = migrate
self._fake_migrate = fake_migrate
self._migrate_enabled = migrate_enabled
self._fake_migrate_all = fake_migrate_all
if self.serializers is not None:
for k, v in self.serializers.items():
serializers._custom_[k] = v
if auto_import or tables:
self.import_table_definitions(adapter.folder, tables=tables)
|
(self, uri='sqlite://dummy.db', pool_size=0, folder=None, db_codec='UTF-8', check_reserved=None, migrate=True, fake_migrate=False, migrate_enabled=True, fake_migrate_all=False, decode_credentials=False, driver_args=None, adapter_args=None, attempts=5, auto_import=False, bigint_id=False, debug=False, lazy_tables=False, db_uid=None, after_connection=None, tables=None, ignore_field_case=True, entity_quoting=True, table_hash=None)
|
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] |
721,570
|
pydal.objects
|
Field
| null |
class Field(Expression, Serializable):
Virtual = FieldVirtual
Method = FieldMethod
Lazy = FieldMethod # for backward compatibility
"""
Represents a database field
Example:
Usage::
a = Field(name, 'string', length=32, default=None, required=False,
requires=IS_NOT_EMPTY(), ondelete='CASCADE',
notnull=False, unique=False,
regex=None, options=None,
uploadfield=True, widget=None, label=None, comment=None,
uploadfield=True, # True means store on disk,
# 'a_field_name' means store in this field in db
# False means file content will be discarded.
writable=True, readable=True, searchable=True, listable=True,
update=None, authorize=None,
autodelete=False, represent=None, uploadfolder=None,
uploadseparate=False # upload to separate directories by uuid_keys
# first 2 character and tablename.fieldname
# False - old behavior
# True - put uploaded file in
# <uploaddir>/<tablename>.<fieldname>/uuid_key[:2]
# directory)
uploadfs=None # a pyfilesystem where to store upload
)
to be used as argument of `DAL.define_table`
"""
def __init__(
self,
fieldname,
type="string",
length=None,
default=DEFAULT,
required=False,
requires=DEFAULT,
ondelete="CASCADE",
onupdate="CASCADE",
notnull=False,
unique=False,
uploadfield=True,
widget=None,
label=None,
comment=None,
writable=True,
readable=True,
searchable=True,
listable=True,
regex=None,
options=None,
update=None,
authorize=None,
autodelete=False,
represent=None,
uploadfolder=None,
uploadseparate=False,
uploadfs=None,
compute=None,
custom_store=None,
custom_retrieve=None,
custom_retrieve_file_properties=None,
custom_delete=None,
filter_in=None,
filter_out=None,
custom_qualifier=None,
map_none=None,
rname=None,
**others,
):
self._db = self.db = None # both for backward compatibility
self.table = self._table = None
self.op = None
self.first = None
self.second = None
if PY2 and isinstance(fieldname, unicode):
try:
fieldname = str(fieldname)
except UnicodeEncodeError:
raise SyntaxError("Field: invalid unicode field name")
self.name = fieldname = cleanup(fieldname)
if (
not isinstance(fieldname, str)
or hasattr(Table, fieldname)
or not REGEX_VALID_TB_FLD.match(fieldname)
or REGEX_PYTHON_KEYWORDS.match(fieldname)
):
raise SyntaxError(
"Field: invalid field name: %s, "
'use rname for "funny" names' % fieldname
)
if not isinstance(type, (Table, Field)):
self.type = type
else:
self.type = "reference %s" % type
self.length = (
length if length is not None else DEFAULTLENGTH.get(self.type, 512)
)
self.default = default if default is not DEFAULT else (update or None)
self.required = required # is this field required
self.ondelete = ondelete.upper() # this is for reference fields only
self.onupdate = onupdate.upper() # this is for reference fields only
self.notnull = notnull
self.unique = unique
# split to deal with decimal(,)
self.regex = regex
if not regex and isinstance(self.type, str):
self.regex = DEFAULT_REGEX.get(self.type.split("(")[0])
self.options = options
self.uploadfield = uploadfield
self.uploadfolder = uploadfolder
self.uploadseparate = uploadseparate
self.uploadfs = uploadfs
self.widget = widget
self.comment = comment
self.writable = writable
self.readable = readable
self.searchable = searchable
self.listable = listable
self.update = update
self.authorize = authorize
self.autodelete = autodelete
self.represent = (
list_represent
if represent is None and type in ("list:integer", "list:string")
else represent
)
self.compute = compute
self.isattachment = True
self.custom_store = custom_store
self.custom_retrieve = custom_retrieve
self.custom_retrieve_file_properties = custom_retrieve_file_properties
self.custom_delete = custom_delete
self.filter_in = filter_in
self.filter_out = filter_out
self.custom_qualifier = custom_qualifier
self.label = label if label is not None else fieldname.replace("_", " ").title()
self.requires = requires if requires is not None else []
self.map_none = map_none
self._rname = self._raw_rname = rname
stype = self.type
if isinstance(self.type, SQLCustomType):
stype = self.type.type
self._itype = REGEX_TYPE.match(stype).group(0) if stype else None
for key in others:
setattr(self, key, others[key])
def bind(self, table):
if self._table is not None:
raise ValueError("Field %s is already bound to a table" % self.longname)
self.db = self._db = table._db
self.table = self._table = table
self.tablename = self._tablename = table._tablename
if self._db and self._rname is None:
self._rname = self._db._adapter.sqlsafe_field(self.name)
self._raw_rname = self.name
def set_attributes(self, *args, **attributes):
self.__dict__.update(*args, **attributes)
return self
def clone(self, point_self_references_to=False, **args):
field = copy.copy(self)
if point_self_references_to and self.type == "reference %s" % self._tablename:
field.type = "reference %s" % point_self_references_to
field.__dict__.update(args)
field.db = field._db = None
field.table = field._table = None
field.tablename = field._tablename = None
if self._db and self._rname == self._db._adapter.sqlsafe_field(self.name):
# Reset the name because it may need to be requoted by bind()
field._rname = field._raw_rname = None
return field
def store(self, file, filename=None, path=None):
# make sure filename is a str sequence
filename = "{}".format(filename)
if self.custom_store:
return self.custom_store(file, filename, path)
if isinstance(file, cgi.FieldStorage):
filename = filename or file.filename
file = file.file
elif not filename:
filename = file.name
filename = os.path.basename(filename.replace("/", os.sep).replace("\\", os.sep))
m = re.search(REGEX_UPLOAD_EXTENSION, filename)
extension = m and m.group(1) or "txt"
uuid_key = self._db.uuid().replace("-", "")[-16:] if self._db else uuidstr()
encoded_filename = to_native(base64.urlsafe_b64encode(to_bytes(filename)))
newfilename = "%s.%s.%s.%s" % (
getattr(self, "_tablename", "no_table"),
self.name,
uuid_key,
encoded_filename,
)
newfilename = (
newfilename[: (self.length - 1 - len(extension))] + "." + extension
)
self_uploadfield = self.uploadfield
if isinstance(self_uploadfield, Field):
blob_uploadfield_name = self_uploadfield.uploadfield
keys = {
self_uploadfield.name: newfilename,
blob_uploadfield
|
(fieldname, type='string', length=None, default=<function <lambda> at 0x7fbac9f848b0>, required=False, requires=<function <lambda> at 0x7fbac9f848b0>, ondelete='CASCADE', onupdate='CASCADE', notnull=False, unique=False, uploadfield=True, widget=None, label=None, comment=None, writable=True, readable=True, searchable=True, listable=True, regex=None, options=None, update=None, authorize=None, autodelete=False, represent=None, uploadfolder=None, uploadseparate=False, uploadfs=None, compute=None, custom_store=None, custom_retrieve=None, custom_retrieve_file_properties=None, custom_delete=None, filter_in=None, filter_out=None, custom_qualifier=None, map_none=None, rname=None, **others)
|
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] |
721,576
|
pydal.objects
|
__getitem__
| null |
def __getitem__(self, i):
if isinstance(i, slice):
start = i.start or 0
stop = i.stop
db = self.db
if start < 0:
pos0 = "(%s - %d)" % (self.len(), abs(start) - 1)
else:
pos0 = start + 1
maxint = sys.maxint if PY2 else sys.maxsize
if stop is None or stop == maxint:
length = self.len()
elif stop < 0:
length = "(%s - %d - %s)" % (self.len(), abs(stop) - 1, pos0)
else:
length = "(%s - %s)" % (stop + 1, pos0)
return Expression(
db, self._dialect.substring, self, (pos0, length), self.type
)
else:
return self[i : i + 1]
|
(self, i)
|
[
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0.01993299275636673
] |
721,579
|
pydal.objects
|
__init__
| null |
def __init__(
self,
fieldname,
type="string",
length=None,
default=DEFAULT,
required=False,
requires=DEFAULT,
ondelete="CASCADE",
onupdate="CASCADE",
notnull=False,
unique=False,
uploadfield=True,
widget=None,
label=None,
comment=None,
writable=True,
readable=True,
searchable=True,
listable=True,
regex=None,
options=None,
update=None,
authorize=None,
autodelete=False,
represent=None,
uploadfolder=None,
uploadseparate=False,
uploadfs=None,
compute=None,
custom_store=None,
custom_retrieve=None,
custom_retrieve_file_properties=None,
custom_delete=None,
filter_in=None,
filter_out=None,
custom_qualifier=None,
map_none=None,
rname=None,
**others,
):
self._db = self.db = None # both for backward compatibility
self.table = self._table = None
self.op = None
self.first = None
self.second = None
if PY2 and isinstance(fieldname, unicode):
try:
fieldname = str(fieldname)
except UnicodeEncodeError:
raise SyntaxError("Field: invalid unicode field name")
self.name = fieldname = cleanup(fieldname)
if (
not isinstance(fieldname, str)
or hasattr(Table, fieldname)
or not REGEX_VALID_TB_FLD.match(fieldname)
or REGEX_PYTHON_KEYWORDS.match(fieldname)
):
raise SyntaxError(
"Field: invalid field name: %s, "
'use rname for "funny" names' % fieldname
)
if not isinstance(type, (Table, Field)):
self.type = type
else:
self.type = "reference %s" % type
self.length = (
length if length is not None else DEFAULTLENGTH.get(self.type, 512)
)
self.default = default if default is not DEFAULT else (update or None)
self.required = required # is this field required
self.ondelete = ondelete.upper() # this is for reference fields only
self.onupdate = onupdate.upper() # this is for reference fields only
self.notnull = notnull
self.unique = unique
# split to deal with decimal(,)
self.regex = regex
if not regex and isinstance(self.type, str):
self.regex = DEFAULT_REGEX.get(self.type.split("(")[0])
self.options = options
self.uploadfield = uploadfield
self.uploadfolder = uploadfolder
self.uploadseparate = uploadseparate
self.uploadfs = uploadfs
self.widget = widget
self.comment = comment
self.writable = writable
self.readable = readable
self.searchable = searchable
self.listable = listable
self.update = update
self.authorize = authorize
self.autodelete = autodelete
self.represent = (
list_represent
if represent is None and type in ("list:integer", "list:string")
else represent
)
self.compute = compute
self.isattachment = True
self.custom_store = custom_store
self.custom_retrieve = custom_retrieve
self.custom_retrieve_file_properties = custom_retrieve_file_properties
self.custom_delete = custom_delete
self.filter_in = filter_in
self.filter_out = filter_out
self.custom_qualifier = custom_qualifier
self.label = label if label is not None else fieldname.replace("_", " ").title()
self.requires = requires if requires is not None else []
self.map_none = map_none
self._rname = self._raw_rname = rname
stype = self.type
if isinstance(self.type, SQLCustomType):
stype = self.type.type
self._itype = REGEX_TYPE.match(stype).group(0) if stype else None
for key in others:
setattr(self, key, others[key])
|
(self, fieldname, type='string', length=None, default=<function <lambda> at 0x7fbac9f848b0>, required=False, requires=<function <lambda> at 0x7fbac9f848b0>, ondelete='CASCADE', onupdate='CASCADE', notnull=False, unique=False, uploadfield=True, widget=None, label=None, comment=None, writable=True, readable=True, searchable=True, listable=True, regex=None, options=None, update=None, authorize=None, autodelete=False, represent=None, uploadfolder=None, uploadseparate=False, uploadfs=None, compute=None, custom_store=None, custom_retrieve=None, custom_retrieve_file_properties=None, custom_delete=None, filter_in=None, filter_out=None, custom_qualifier=None, map_none=None, rname=None, **others)
|
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] |
721,580
|
pydal.objects
|
__invert__
| null |
def __invert__(self):
if hasattr(self, "_op") and self.op == self._dialect.invert:
return self.first
return Expression(self.db, self._dialect.invert, self, type=self.type)
|
(self)
|
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