Bio.Phylo.PhyloXMLIO module¶
PhyloXML reader/parser, writer, and associated functions.
Instantiates tree elements from a parsed PhyloXML file, and constructs an XML
file from a Bio.Phylo.PhyloXML
object.
- About capitalization:
phyloXML means the file format specification
PhyloXML means the Biopython module
Bio.Phylo.PhyloXML
and its classesPhyloxml means the top-level class used by
PhyloXMLIO.read
(but notBio.Phylo.read
!), containing a list of Phylogenies (objects derived fromBaseTree.Tree
)
-
exception
Bio.Phylo.PhyloXMLIO.
PhyloXMLError
¶ Bases:
Exception
Exception raised when PhyloXML object construction cannot continue.
XML syntax errors will be found and raised by the underlying ElementTree module; this exception is for valid XML that breaks the phyloXML specification.
-
Bio.Phylo.PhyloXMLIO.
read
(file)¶ Parse a phyloXML file or stream and build a tree of Biopython objects.
The children of the root node are phylogenies and possibly other arbitrary (non-phyloXML) objects.
- Returns
a single
Bio.Phylo.PhyloXML.Phyloxml
object.
-
Bio.Phylo.PhyloXMLIO.
parse
(file)¶ Iterate over the phylogenetic trees in a phyloXML file.
This ignores any additional data stored at the top level, but may be more memory-efficient than the
read
function.- Returns
a generator of
Bio.Phylo.PhyloXML.Phylogeny
objects.
-
Bio.Phylo.PhyloXMLIO.
write
(obj, file, encoding='unicode', indent=True)¶ Write a phyloXML file.
- Parameters
- obj
an instance of
Phyloxml
,Phylogeny
orBaseTree.Tree
, or an iterable of either of the latter two. The object will be converted to a Phyloxml object before serialization.- file
either an open handle or a file name.
-
class
Bio.Phylo.PhyloXMLIO.
Parser
(file)¶ Bases:
object
Methods for parsing all phyloXML nodes from an XML stream.
To minimize memory use, the tree of ElementTree parsing events is cleared after completing each phylogeny, clade, and top-level ‘other’ element. Elements below the clade level are kept in memory until parsing of the current clade is finished – this shouldn’t be a problem because clade is the only recursive element, and non-clade nodes below this level are of bounded size.
-
__init__
(self, file)¶ Initialize the class.
-
read
(self)¶ Parse the phyloXML file and create a single Phyloxml object.
-
parse
(self)¶ Parse the phyloXML file incrementally and return each phylogeny.
-
other
(self, elem, namespace, localtag)¶ Create an Other object, a non-phyloXML element.
-
accession
(self, elem)¶ Create accession object.
-
annotation
(self, elem)¶ Create annotation object.
-
binary_characters
(self, elem)¶ Create binary characters object.
-
clade_relation
(self, elem)¶ Create clade relationship object.
-
color
(self, elem)¶ Create branch color object.
-
confidence
(self, elem)¶ Create confidence object.
-
date
(self, elem)¶ Create date object.
-
distribution
(self, elem)¶ Create geographic distribution object.
-
domain
(self, elem)¶ Create protein domain object.
-
domain_architecture
(self, elem)¶ Create domain architecture object.
-
events
(self, elem)¶ Create events object.
-
id
(self, elem)¶ Create identifier object.
-
mol_seq
(self, elem)¶ Create molecular sequence object.
-
point
(self, elem)¶ Create point object, coordinates of a point.
-
polygon
(self, elem)¶ Create polygon object, list of points.
-
property
(self, elem)¶ Create properties from external resources.
-
reference
(self, elem)¶ Create literature reference object.
-
sequence_relation
(self, elem)¶ Create sequence relationship object, relationship between two sequences.
-
uri
(self, elem)¶ Create uri object, expected to be a url.
-
-
class
Bio.Phylo.PhyloXMLIO.
Writer
(phyloxml)¶ Bases:
object
Methods for serializing a PhyloXML object to XML.
-
__init__
(self, phyloxml)¶ Build an ElementTree from a PhyloXML object.
-
write
(self, file, encoding='unicode', indent=True)¶ Write PhyloXML to a file.
-
phyloxml
(self, obj)¶ Convert phyloxml to Etree element.
-
other
(self, obj)¶ Convert other to Etree element.
-
phylogeny
(self, obj)¶ Serialize a phylogeny and its subnodes, in order.
-
clade
(self, obj)¶ Serialize a clade and its subnodes, in order.
-
accession
(self, obj)¶ Serialize a accession and its subnodes, in order.
-
annotation
(self, obj)¶ Serialize a annotation and its subnodes, in order.
-
binary_characters
(self, obj)¶ Serialize a binary_characters node and its subnodes.
-
clade_relation
(self, obj)¶ Serialize a clade_relation and its subnodes, in order.
-
color
(self, obj)¶ Serialize a color and its subnodes, in order.
-
confidence
(self, obj)¶ Serialize a confidence and its subnodes, in order.
-
date
(self, obj)¶ Serialize a date and its subnodes, in order.
-
distribution
(self, obj)¶ Serialize a distribution and its subnodes, in order.
-
domain
(self, obj)¶ Serialize a domain node.
-
domain_architecture
(self, obj)¶ Serialize a domain_architecture and its subnodes, in order.
-
events
(self, obj)¶ Serialize a events and its subnodes, in order.
-
id
(self, obj)¶ Serialize a id and its subnodes, in order.
-
mol_seq
(self, obj)¶ Serialize a mol_seq and its subnodes, in order.
-
node_id
(self, obj)¶ Serialize a node_id and its subnodes, in order.
-
point
(self, obj)¶ Serialize a point and its subnodes, in order.
-
polygon
(self, obj)¶ Serialize a polygon and its subnodes, in order.
-
property
(self, obj)¶ Serialize a property and its subnodes, in order.
-
reference
(self, obj)¶ Serialize a reference and its subnodes, in order.
-
sequence
(self, obj)¶ Serialize a sequence and its subnodes, in order.
-
sequence_relation
(self, obj)¶ Serialize a sequence_relation and its subnodes, in order.
-
taxonomy
(self, obj)¶ Serialize a taxonomy and its subnodes, in order.
-
uri
(self, obj)¶ Serialize a uri and its subnodes, in order.
-
alt
(self, obj)¶ Serialize a simple alt node.
-
branch_length
(self, obj)¶ Serialize a simple branch_length node.
-
lat
(self, obj)¶ Serialize a simple lat node.
-
long
(self, obj)¶ Serialize a simple long node.
-
maximum
(self, obj)¶ Serialize a simple maximum node.
-
minimum
(self, obj)¶ Serialize a simple minimum node.
-
value
(self, obj)¶ Serialize a simple value node.
-
width
(self, obj)¶ Serialize a simple width node.
-
blue
(self, obj)¶ Serialize a simple blue node.
-
duplications
(self, obj)¶ Serialize a simple duplications node.
-
green
(self, obj)¶ Serialize a simple green node.
-
losses
(self, obj)¶ Serialize a simple losses node.
-
red
(self, obj)¶ Serialize a simple red node.
-
speciations
(self, obj)¶ Serialize a simple speciations node.
-
bc
(self, obj)¶ Serialize a simple bc node.
-
code
(self, obj)¶ Serialize a simple code node.
-
common_name
(self, obj)¶ Serialize a simple common_name node.
-
desc
(self, obj)¶ Serialize a simple desc node.
-
description
(self, obj)¶ Serialize a simple description node.
-
location
(self, obj)¶ Serialize a simple location node.
-
name
(self, obj)¶ Serialize a simple name node.
-
rank
(self, obj)¶ Serialize a simple rank node.
-
scientific_name
(self, obj)¶ Serialize a simple scientific_name node.
-
symbol
(self, obj)¶ Serialize a simple symbol node.
-
synonym
(self, obj)¶ Serialize a simple synonym node.
-
type
(self, obj)¶ Serialize a simple type node.
-