Bio.Phylo.PhyloXML module

Classes corresponding to phyloXML elements.

See Also

Official specification:: http://phyloxml.org/
Journal article:: Han and Zmasek (2009), https://doi.org/10.1186/1471-2105-10-356

exception Bio.Phylo.PhyloXML.PhyloXMLWarning

Bases: Bio.BiopythonWarning

Warning for non-compliance with the phyloXML specification.

class Bio.Phylo.PhyloXML.PhyloElement

Bases: Bio.Phylo.BaseTree.TreeElement

Base class for all PhyloXML objects.

class Bio.Phylo.PhyloXML.Phyloxml(attributes, phylogenies=None, other=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Root node of the PhyloXML document.

Contains an arbitrary number of Phylogeny elements, possibly followed by elements from other namespaces.

Parameters

attributesdict: (XML namespace definitions)
phylogenieslist: The phylogenetic trees
otherlist: Arbitrary non-phyloXML elements, if any

__init__(attributes, phylogenies=None, other=None): Initialize parameters for PhyloXML object.

__getitem__(index): Get a phylogeny by index or name.

__iter__(): Iterate through the phylogenetic trees in this object.

__len__(): Return the number of phylogenetic trees in this object.

__str__(): Return name of phylogenies in the object.

class Bio.Phylo.PhyloXML.Other(tag, namespace=None, attributes=None, value=None, children=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Container for non-phyloXML elements in the tree.

Usually, an Other object will have either a ‘value’ or a non-empty list of ‘children’, but not both. This is not enforced here, though.

Parameters

tagstring: local tag for the XML node
namespacestring: XML namespace for the node – should not be the default phyloXML namespace.
attributesdict of strings: attributes on the XML node
valuestring: text contained directly within this XML node
childrenlist: child nodes, if any (also Other instances)

__init__(tag, namespace=None, attributes=None, value=None, children=None): Initialize values for non-phyloXML elements.

__iter__(): Iterate through the children of this object (if any).

class Bio.Phylo.PhyloXML.Phylogeny(root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement, Bio.Phylo.BaseTree.Tree

A phylogenetic tree.

Parameters

rootClade: the root node/clade of this tree
rootedbool: True if this tree is rooted
rerootablebool: True if this tree is rerootable
branch_length_unitstring: unit for branch_length values on clades
namestring: identifier for this tree, not required to be unique
idId: unique identifier for this tree
descriptionstring: plain-text description
dateDate: date for the root node of this tree
confidenceslist: Confidence objects for this tree
clade_relationslist: CladeRelation objects
sequence_relationslist: SequenceRelation objects
propertieslist: Property objects
otherlist: non-phyloXML elements (type Other)

__init__(root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, name=None, id=None, description=None, date=None, confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None): Initialize values for phylogenetic tree object.

classmethod from_tree(tree, **kwargs)

Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree).

Keyword arguments are the usual Phylogeny constructor parameters.

classmethod from_clade(clade, **kwargs)

Create a new Phylogeny given a Newick or BaseTree Clade object.

Keyword arguments are the usual PhyloXML.Clade constructor parameters.

as_phyloxml()

Return this tree, a PhyloXML-compatible Phylogeny object.

Overrides the BaseTree method.

to_phyloxml_container(**kwargs): Create a new Phyloxml object containing just this phylogeny.

to_alignment(): Construct a MultipleSeqAlignment from the aligned sequences in this tree.

property alignment: Construct an Alignment object from the aligned sequences in this tree.

property confidence

Equivalent to self.confidences[0] if there is only 1 value (PRIVATE).

See Also: Clade.confidence, Clade.taxonomy

class Bio.Phylo.PhyloXML.Clade(branch_length=None, id_source=None, name=None, width=None, color=None, node_id=None, events=None, binary_characters=None, date=None, confidences=None, taxonomies=None, sequences=None, distributions=None, references=None, properties=None, clades=None, other=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement, Bio.Phylo.BaseTree.Clade

Describes a branch of the current phylogenetic tree.

Used recursively, describes the topology of a phylogenetic tree.

Both color and width elements should be interpreted by client code as applying to the whole clade, including all descendents, unless overwritten in-sub clades. This module doesn’t automatically assign these attributes to sub-clades to achieve this cascade – and neither should you.

Parameters

branch_length: parent branch length of this clade
id_source: link other elements to a clade (on the xml-level)
namestring: short label for this clade
confidenceslist of Confidence objects: used to indicate the support for a clade/parent branch.
widthfloat: branch width for this clade (including branch from parent)
colorBranchColor: color used for graphical display of this clade
node_id: unique identifier for the root node of this clade
taxonomieslist: Taxonomy objects
sequenceslist: Sequence objects
eventsEvents: describe such events as gene-duplications at the root node/parent branch of this clade
binary_charactersBinaryCharacters: binary characters
distributionslist of Distribution objects: distribution(s) of this clade
dateDate: a date for the root node of this clade
referenceslist: Reference objects
propertieslist: Property objects
cladeslist Clade objects: Sub-clades
otherlist of Other objects: non-phyloXML objects

__init__(branch_length=None, id_source=None, name=None, width=None, color=None, node_id=None, events=None, binary_characters=None, date=None, confidences=None, taxonomies=None, sequences=None, distributions=None, references=None, properties=None, clades=None, other=None): Initialize value for the Clade object.

classmethod from_clade(clade, **kwargs)

Create a new PhyloXML Clade from a Newick or BaseTree Clade object.

Keyword arguments are the usual PhyloXML Clade constructor parameters.

to_phylogeny(**kwargs): Create a new phylogeny containing just this clade.

property confidence: Return confidence values (PRIVATE).

property taxonomy: Get taxonomy list for the clade (PRIVATE).

class Bio.Phylo.PhyloXML.BranchColor(*args, **kwargs)

Bases: Bio.Phylo.PhyloXML.PhyloElement, Bio.Phylo.BaseTree.BranchColor

Manage Tree branch’s color.

__init__(*args, **kwargs): Initialize parameters for the BranchColor object.

class Bio.Phylo.PhyloXML.Accession(value, source)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Captures the local part in a sequence identifier.

Example: In UniProtKB:P17304, the Accession instance attribute value is ‘P17304’ and the source attribute is ‘UniProtKB’.

__init__(value, source): Initialize value for Accession object.

__str__(): Show the class name and an identifying attribute.

class Bio.Phylo.PhyloXML.Annotation(ref=None, source=None, evidence=None, type=None, desc=None, confidence=None, uri=None, properties=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

The annotation of a molecular sequence.

It is recommended to annotate by using the optional ‘ref’ attribute.

Parameters

refstring: reference string, e.g. ‘GO:0008270’, ‘KEGG:Tetrachloroethene degradation’, ‘EC:1.1.1.1’
sourcestring: plain-text source for this annotation
evidencestr: describe evidence as free text (e.g. ‘experimental’)
descstring: free text description
confidenceConfidence: state the type and value of support (type Confidence)
propertieslist: typed and referenced annotations from external resources
uriUri: link

re_ref = re.compile('[a-zA-Z0-9_]+:[a-zA-Z0-9_\\.\\-\\s]+')

__init__(ref=None, source=None, evidence=None, type=None, desc=None, confidence=None, uri=None, properties=None): Initialize value for the Annotation object.

class Bio.Phylo.PhyloXML.BinaryCharacters(type=None, gained_count=None, lost_count=None, present_count=None, absent_count=None, gained=None, lost=None, present=None, absent=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Binary characters at the root of a clade.

The names and/or counts of binary characters present, gained, and lost at the root of a clade.

__init__(type=None, gained_count=None, lost_count=None, present_count=None, absent_count=None, gained=None, lost=None, present=None, absent=None): Initialize values for the BinaryCharacters object.

class Bio.Phylo.PhyloXML.CladeRelation(type, id_ref_0, id_ref_1, distance=None, confidence=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Expresses a typed relationship between two clades.

For example, this could be used to describe multiple parents of a clade.

__init__(type, id_ref_0, id_ref_1, distance=None, confidence=None): Initialize values for the CladeRelation object.

class Bio.Phylo.PhyloXML.Confidence(value, type='unknown')

Bases: float, Bio.Phylo.PhyloXML.PhyloElement

A general purpose confidence element.

For example, this can be used to express the bootstrap support value of a clade (in which case the type attribute is ‘bootstrap’).

Parameters

valuefloat: confidence value
typestring: label for the type of confidence, e.g. ‘bootstrap’

static __new__(cls, value, type='unknown'): Create and return a Confidence object with the specified value and type.

property value: Return the float value of the Confidence object.

class Bio.Phylo.PhyloXML.Date(value=None, unit=None, desc=None, minimum=None, maximum=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

A date associated with a clade/node.

Its value can be numerical by using the ‘value’ element and/or free text with the ‘desc’ element’ (e.g. ‘Silurian’). If a numerical value is used, it is recommended to employ the ‘unit’ attribute.

Parameters

unitstring: type of numerical value (e.g. ‘mya’ for ‘million years ago’)
valuefloat: the date value
descstring: plain-text description of the date
minimumfloat: lower bound on the date value
maximumfloat: upper bound on the date value

__init__(value=None, unit=None, desc=None, minimum=None, maximum=None): Initialize values of the Date object.

__str__(): Show the class name and the human-readable date.

class Bio.Phylo.PhyloXML.Distribution(desc=None, points=None, polygons=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Geographic distribution of the items of a clade (species, sequences).

Intended for phylogeographic applications.

Parameters

descstring: free-text description of the location
pointslist of Point objects: coordinates (similar to the ‘Point’ element in Google’s KML format)
polygonslist of Polygon objects: coordinate sets defining geographic regions

__init__(desc=None, points=None, polygons=None): Initialize values of Distribution object.

class Bio.Phylo.PhyloXML.DomainArchitecture(length=None, domains=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Domain architecture of a protein.

Parameters

lengthint: total length of the protein sequence
domainslist ProteinDomain objects: the domains within this protein

__init__(length=None, domains=None): Initialize values of the DomainArchitecture object.

class Bio.Phylo.PhyloXML.Events(type=None, duplications=None, speciations=None, losses=None, confidence=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Events at the root node of a clade (e.g. one gene duplication).

All attributes are set to None by default, but this object can also be treated as a dictionary, in which case None values are treated as missing keys and deleting a key resets that attribute’s value back to None.

ok_type = {'fusion', 'mixed', 'other', 'speciation_or_duplication', 'transfer', 'unassigned'}

__init__(type=None, duplications=None, speciations=None, losses=None, confidence=None): Initialize values of the Events object.

items(): Return Event’s items.

keys(): Return Event’s keys.

values(): Return values from a key-value pair in an Events dict.

__len__(): Return number of Events.

__getitem__(key): Get value of Event with the given key.

__setitem__(key, val): Add item to Event dict.

__delitem__(key): Delete Event with given key.

__iter__(): Iterate over the keys present in a Events dict.

__contains__(key): Return True if Event dict contains key.

class Bio.Phylo.PhyloXML.Id(value, provider=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

A general-purpose identifier element.

Allows to indicate the provider (or authority) of an identifier, e.g. NCBI, along with the value itself.

__init__(value, provider=None): Initialize values for the identifier object.

__str__(): Return identifier as a string.

class Bio.Phylo.PhyloXML.MolSeq(value, is_aligned=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Store a molecular sequence.

Parameters

valuestring: the sequence itself
is_alignedbool: True if this sequence is aligned with the others (usually meaning all aligned seqs are the same length and gaps may be present)

re_value = re.compile('[a-zA-Z\\.\\-\\?\\*_]+')

__init__(value, is_aligned=None): Initialize parameters for the MolSeq object.

__str__(): Return the value of the Molecular Sequence object.

class Bio.Phylo.PhyloXML.Point(geodetic_datum, lat, long, alt=None, alt_unit=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Geographic coordinates of a point, with an optional altitude.

Used by element ‘Distribution’.

Parameters

geodetic_datumstring, required: the geodetic datum (also called ‘map datum’). For example, Google’s KML uses ‘WGS84’.
latnumeric: latitude
longnumeric: longitude
altnumeric: altitude
alt_unitstring: unit for the altitude (e.g. ‘meter’)

__init__(geodetic_datum, lat, long, alt=None, alt_unit=None): Initialize value for the Point object.

class Bio.Phylo.PhyloXML.Polygon(points=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

A polygon defined by a list of ‘Points’ (used by element ‘Distribution’).

Parameters: points – list of 3 or more points representing vertices.

__init__(points=None): Initialize value for the Polygon object.

__str__(): Return list of points as a string.

class Bio.Phylo.PhyloXML.Property(value, ref, applies_to, datatype, unit=None, id_ref=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

A typed and referenced property from an external resources.

Can be attached to Phylogeny, Clade, and Annotation objects.

Parameters

valuestring: the value of the property
refstring: reference to an external resource, e.g. “NOAA:depth”
applies_tostring: indicates the item to which a property applies to (e.g. ‘node’ for the parent node of a clade, ‘parent_branch’ for the parent branch of a clade, or just ‘clade’).
datatypestring: the type of a property; limited to xsd-datatypes (e.g. ‘xsd:string’, ‘xsd:boolean’, ‘xsd:integer’, ‘xsd:decimal’, ‘xsd:float’, ‘xsd:double’, ‘xsd:date’, ‘xsd:anyURI’).
unitstring (optional): the unit of the property, e.g. “METRIC:m”
id_refId (optional): allows to attached a property specifically to one element (on the xml-level)

re_ref = re.compile('[a-zA-Z0-9_]+:[a-zA-Z0-9_\\.\\-\\s]+')

ok_applies_to = {'annotation', 'clade', 'node', 'other', 'parent_branch', 'phylogeny'}

ok_datatype = {'xsd:anyURI', 'xsd:base64Binary', 'xsd:boolean', 'xsd:byte', 'xsd:date', 'xsd:dateTime', 'xsd:decimal', 'xsd:double', 'xsd:duration', 'xsd:float', 'xsd:gDay', 'xsd:gMonth', 'xsd:gMonthDay', 'xsd:gYear', 'xsd:gYearMonth', 'xsd:hexBinary', 'xsd:int', 'xsd:integer', 'xsd:long', 'xsd:negativeInteger', 'xsd:nonNegativeInteger', 'xsd:nonPositiveInteger', 'xsd:normalizedString', 'xsd:positiveInteger', 'xsd:short', 'xsd:string', 'xsd:time', 'xsd:token', 'xsd:unsignedByte', 'xsd:unsignedInt', 'xsd:unsignedLong', 'xsd:unsignedShort'}

__init__(value, ref, applies_to, datatype, unit=None, id_ref=None): Initialize value for the Property object.

class Bio.Phylo.PhyloXML.ProteinDomain(value, start, end, confidence=None, id=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Represents an individual domain in a domain architecture.

The locations use 0-based indexing, as most Python objects including SeqFeature do, rather than the usual biological convention starting at 1. This means the start and end attributes can be used directly as slice indexes on Seq objects.

Parameters

startnon-negative integer: start of the domain on the sequence, using 0-based indexing
endnon-negative integer: end of the domain on the sequence
confidencefloat: can be used to store e.g. E-values
idstring: unique identifier/name

__init__(value, start, end, confidence=None, id=None): Initialize value for a ProteinDomain object.

classmethod from_seqfeature(feat): Create ProteinDomain object from SeqFeature.

to_seqfeature(): Create a SeqFeature from the ProteinDomain Object.

class Bio.Phylo.PhyloXML.Reference(doi=None, desc=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Literature reference for a clade.

NB: Whenever possible, use the doi attribute instead of the free-text desc element.

re_doi = re.compile('[a-zA-Z0-9_\\.]+/[a-zA-Z0-9_\\.]+')

__init__(doi=None, desc=None): Initialize elements of the Reference class object.

class Bio.Phylo.PhyloXML.Sequence(type=None, id_ref=None, id_source=None, symbol=None, accession=None, name=None, location=None, mol_seq=None, uri=None, domain_architecture=None, annotations=None, other=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

A molecular sequence (Protein, DNA, RNA) associated with a node.

One intended use for id_ref is to link a sequence to a taxonomy (via the taxonomy’s id_source) in case of multiple sequences and taxonomies per node.

Parameters

type{‘dna’, ‘rna’, ‘protein’}: type of molecule this sequence represents
id_refstring: reference to another resource
id_sourcestring: source for the reference
symbolstring: short symbol of the sequence, e.g. ‘ACTM’ (max. 10 chars)
accessionAccession: accession code for this sequence.
namestring: full name of the sequence, e.g. ‘muscle Actin’
location: location of a sequence on a genome/chromosome.
mol_seqMolSeq: the molecular sequence itself
uriUri: link
annotationslist of Annotation objects: annotations on this sequence
domain_architectureDomainArchitecture: protein domains on this sequence
otherlist of Other objects: non-phyloXML elements

types = {'dna', 'protein', 'rna'}

re_symbol = re.compile('\\S{1,10}')

__init__(type=None, id_ref=None, id_source=None, symbol=None, accession=None, name=None, location=None, mol_seq=None, uri=None, domain_architecture=None, annotations=None, other=None): Initialize value for a Sequence object.

classmethod from_seqrecord(record, is_aligned=None): Create a new PhyloXML Sequence from a SeqRecord object.

to_seqrecord()

Create a SeqRecord object from this Sequence instance.

The seqrecord.annotations dictionary is packed like so:

{ # Sequence attributes with no SeqRecord equivalent:
  'id_ref': self.id_ref,
  'id_source': self.id_source,
  'location': self.location,
  'uri': { 'value': self.uri.value,
                  'desc': self.uri.desc,
                  'type': self.uri.type },
  # Sequence.annotations attribute (list of Annotations)
  'annotations': [{'ref': ann.ref,
                   'source': ann.source,
                   'evidence': ann.evidence,
                   'type': ann.type,
                   'confidence': [ann.confidence.value,
                                  ann.confidence.type],
                   'properties': [{'value': prop.value,
                                    'ref': prop.ref,
                                    'applies_to': prop.applies_to,
                                    'datatype': prop.datatype,
                                    'unit': prop.unit,
                                    'id_ref': prop.id_ref}
                                   for prop in ann.properties],
                  } for ann in self.annotations],
}

class Bio.Phylo.PhyloXML.SequenceRelation(type, id_ref_0, id_ref_1, distance=None, confidence=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Express a typed relationship between two sequences.

For example, this could be used to describe an orthology (in which case attribute ‘type’ is ‘orthology’).

Parameters

id_ref_0Id: first sequence reference identifier
id_ref_1Id: second sequence reference identifier
distancefloat: distance between the two sequences
typerestricted string: describe the type of relationship
confidenceConfidence: confidence value for this relation

ok_type = {'one_to_one_orthology', 'orthology', 'other', 'paralogy', 'super_orthology', 'ultra_paralogy', 'unknown', 'xenology'}

__init__(type, id_ref_0, id_ref_1, distance=None, confidence=None): Initialize the class.

class Bio.Phylo.PhyloXML.Taxonomy(id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

Describe taxonomic information for a clade.

Parameters

id_sourceId: link other elements to a taxonomy (on the XML level)
idId: unique identifier of a taxon, e.g. Id(‘6500’, provider=’ncbi_taxonomy’) for the California sea hare
coderestricted string: store UniProt/Swiss-Prot style organism codes, e.g. ‘APLCA’ for the California sea hare ‘Aplysia californica’
scientific_namestring: the standard scientific name for this organism, e.g. ‘Aplysia californica’ for the California sea hare
authoritystring: keep the authority, such as ‘J. G. Cooper, 1863’, associated with the ‘scientific_name’
common_nameslist of strings: common names for this organism
synonymslist of strings: synonyms for this taxon?
rankrestricted string: taxonomic rank
uriUri: link
otherlist of Other objects: non-phyloXML elements

re_code = re.compile('[a-zA-Z0-9_]{2,10}')

ok_rank = {'branch', 'class', 'cohort', 'cultivar', 'division', 'domain', 'family', 'form', 'genus', 'infraclass', 'infracohort', 'infradivision', 'infrakingdom', 'infralegion', 'infraphylum', 'infratribe', 'kingdom', 'legion', 'microphylum', 'order', 'other', 'phylum', 'species', 'subclass', 'subcohort', 'subdivision', 'subfamily', 'subform', 'subgenus', 'subkingdom', 'sublegion', 'suborder', 'subphylum', 'subspecies', 'subtribe', 'subvariety', 'superclass', 'supercohort', 'superdivision', 'superfamily', 'superlegion', 'superorder', 'superphylum', 'superspecies', 'supertribe', 'tribe', 'unknown', 'variety'}

__init__(id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None): Initialize the class.

__str__(): Show the class name and an identifying attribute.

class Bio.Phylo.PhyloXML.Uri(value, desc=None, type=None)

Bases: Bio.Phylo.PhyloXML.PhyloElement

A uniform resource identifier.

In general, this is expected to be an URL (for example, to link to an image on a website, in which case the type attribute might be ‘image’ and desc might be ‘image of a California sea hare’).

__init__(value, desc=None, type=None): Initialize the class.

__str__(): Return string representation of Uri.