# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com) # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Classes corresponding to phyloXML elements. See U{ http://phyloxml.org/ } for the official specification. See also Han and Zmasek (2009) doi:10.1186/1471-2105-10-356 """ __docformat__ = "epytext en" import re import warnings from Bio import Alphabet from Bio.Align import MultipleSeqAlignment from Bio.Seq import Seq from Bio.SeqFeature import SeqFeature, FeatureLocation from Bio.SeqRecord import SeqRecord from Bio.Phylo import BaseTree class PhyloXMLWarning(Warning): """Warning for non-compliance with the phyloXML specification.""" pass def _check_str(text, testfunc): """Check a string using testfunc, and warn if there's no match.""" if text is not None and not testfunc(text): warnings.warn("String %s doesn't match the given regexp" % text, PhyloXMLWarning, stacklevel=2) # Core elements class PhyloElement(BaseTree.TreeElement): """Base class for all PhyloXML objects.""" class Phyloxml(PhyloElement): """Root node of the PhyloXML document. Contains an arbitrary number of Phylogeny elements, possibly followed by elements from other namespaces. @param attributes: (XML namespace definitions) @param phylogenies: list of phylogenetic trees @param other: list of arbitrary non-phyloXML elements, if any """ def __init__(self, attributes, phylogenies=None, other=None): self.attributes = attributes self.phylogenies = phylogenies or [] self.other = other or [] def __getitem__(self, index): """Get a phylogeny by index or name.""" if isinstance(index, int) or isinstance(index, slice): return self.phylogenies[index] if not isinstance(index, basestring): raise KeyError("can't use %s as an index" % type(index)) for tree in self.phylogenies: if tree.name == index: return tree else: raise KeyError("no phylogeny found with name " + repr(index)) def __iter__(self): """Iterate through the phylogenetic trees in this object.""" return iter(self.phylogenies) def __len__(self): """Number of phylogenetic trees in this object.""" return len(self.phylogenies) def __str__(self): return '%s([%s])' % (self.__class__.__name__, ',\n'.join(map(str, self.phylogenies))) class Other(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. @param tag: local tag for the XML node @param namespace: XML namespace for the node -- should not be the default phyloXML namespace. @param attributes: string attributes on the XML node @param value: text contained directly within this XML node @param children: list of child nodes, if any (also Other instances) """ def __init__(self, tag, namespace=None, attributes=None, value=None, children=None): self.tag = tag self.namespace = namespace self.attributes = attributes self.value = value self.children = children or [] def __iter__(self): """Iterate through the children of this object (if any).""" return iter(self.children) class Phylogeny(PhyloElement, BaseTree.Tree): """A phylogenetic tree. @param root: the root node/clade of this tree @param rooted: True if this tree is rooted @param rerootable: True if this tree is rerootable @param branch_length_unit: unit for branch_length values on clades @type type: str @param name: string identifier for this tree, not required to be unique @param id: unique identifier for this tree (type Id) @param description: plain-text description @param date: date for the root node of this tree (type Date) @param confidences: list of Confidence objects for this tree @param clade_relations: list of CladeRelation objects @param sequence_relations: list of SequenceRelation objects @param properties: list of Property objects @param other: list of non-phyloXML elements (type Other) """ def __init__(self, root=None, rooted=True, rerootable=None, branch_length_unit=None, type=None, # Child nodes name=None, id=None, description=None, date=None, # Collections confidences=None, clade_relations=None, sequence_relations=None, properties=None, other=None, ): assert isinstance(rooted, bool) self.root = root self.rooted = rooted self.rerootable = rerootable self.branch_length_unit = branch_length_unit self.type = type self.name = name self.id = id self.description = description self.date = date self.confidences = confidences or [] self.clade_relations = clade_relations or [] self.sequence_relations = sequence_relations or [] self.properties = properties or [] self.other = other or [] @classmethod def from_tree(cls, tree, **kwargs): """Create a new Phylogeny given a Tree (from Newick/Nexus or BaseTree). Keyword arguments are the usual Phylogeny constructor parameters. """ phy = cls( root=Clade.from_clade(tree.root), rooted=tree.rooted, name=tree.name, id=(tree.id is not None) and Id(str(tree.id)) or None) phy.__dict__.update(kwargs) return phy @classmethod def from_clade(cls, clade, **kwargs): """Create a new Phylogeny given a Newick or BaseTree Clade object. Keyword arguments are the usual PhyloXML Clade constructor parameters. """ return Clade.from_clade(clade).to_phylogeny(**kwargs) # XXX Backward compatibility shim -- remove in Biopython 1.56 @classmethod def from_subtree(cls, clade, **kwargs): """DEPRECATED: use from_clade() instead.""" warnings.warn("use from_clade() instead.""", DeprecationWarning, stacklevel=2) return cls.from_clade(clade, **kwargs) def as_phyloxml(self): """Return this tree, a PhyloXML-compatible Phylogeny object. Overrides the BaseTree method. """ return self # XXX Backward compatibility shim -- remove in Biopython 1.56 def to_phyloxml(self, **kwargs): """DEPRECATED: use to_phyloxml_container instead.""" warnings.warn("use to_phyloxml_container() instead.""", DeprecationWarning, stacklevel=2) return self.to_phyloxml_container(**kwargs) def to_phyloxml_container(self, **kwargs): """Create a new Phyloxml object containing just this phylogeny.""" return Phyloxml(kwargs, phylogenies=[self]) def to_alignment(self): """Construct an alignment from the aligned sequences in this tree.""" def is_aligned_seq(elem): if isinstance(elem, Sequence) and elem.mol_seq.is_aligned: return True return False seqs = self._filter_search(is_aligned_seq, 'preorder', True) try: first_seq = seqs.next() except StopIteration: # No aligned sequences were found --> empty MSA return MultipleSeqAlignment([]) msa = MultipleSeqAlignment([first_seq.to_seqrecord()], first_seq.get_alphabet()) msa.extend(seq.to_seqrecord() for seq in seqs) return msa # Singular property for plural attribute def _get_confidence(self): """Equivalent to self.confidences[0] if there is only 1 value. See also: Clade.confidence, Clade.taxonomy """ if len(self.confidences) == 0: return None if len(self.confidences) > 1: raise AttributeError("more than 1 confidence value available; " "use Phylogeny.confidences") return self.confidences[0] def _set_confidence(self, value): if isinstance(value, float) or isinstance(value, int): value = Confidence(value) elif not isinstance(value, Confidence): raise ValueError("value must be a number or Confidence instance") if len(self.confidences) == 0: self.confidences.append(value) elif len(self.confidences) == 1: self.confidences[0] = value else: raise ValueError("multiple confidence values already exist; " "use Phylogeny.confidences instead") confidence = property(_get_confidence, _set_confidence) class Clade(PhyloElement, 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. @param branch_length: parent branch length of this clade @param id_source: link other elements to a clade (on the xml-level) @param name: short string label for this clade @param confidences: list of Confidence objects, used to indicate the support for a clade/parent branch. @param width: branch width for this clade (including branch from parent) @param color: color used for graphical display of this clade @param node_id: unique identifier for the root node of this clade @param taxonomies: list of Taxonomy objects @param sequences: list of Sequence objects @param events: describe such events as gene-duplications at the root node/parent branch of this clade @param binary_characters: a BinaryCharacters object @param distributions: list of Distribution objects @param date: a date for the root node of this clade (type Date) @param references: list of Reference objects @param properties: list of Property objects @param clades: list of sub-clades (type Clade) @param other: list of non-phyloXML objects """ def __init__(self, # Attributes branch_length=None, id_source=None, # Child nodes name=None, width=None, color=None, node_id=None, events=None, binary_characters=None, date=None, # Collections confidences=None, taxonomies=None, sequences=None, distributions=None, references=None, properties=None, clades=None, other=None, ): self.branch_length = branch_length self.id_source = id_source self.name = name self.width = width self.color = color self.node_id = node_id self.events = events self.binary_characters = binary_characters self.date = date self.confidences = confidences or [] self.taxonomies = taxonomies or [] self.sequences = sequences or [] self.distributions = distributions or [] self.references = references or [] self.properties = properties or [] self.clades = clades or [] self.other = other or [] @classmethod def from_clade(cls, clade, **kwargs): """Create a new PhyloXML Clade from a Newick or BaseTree Clade object. Keyword arguments are the usual PhyloXML Clade constructor parameters. """ new_clade = cls(branch_length=clade.branch_length, name=clade.name) new_clade.clades = [cls.from_clade(c) for c in clade] new_clade.__dict__.update(kwargs) return new_clade # XXX Backward compatibility shim -- remove in Biopython 1.56 @classmethod def from_subtree(cls, clade, **kwargs): """DEPRECATED: use from_clade() instead.""" warnings.warn("use from_clade() instead.""", DeprecationWarning, stacklevel=2) return cls.from_clade(clade, **kwargs) def to_phylogeny(self, **kwargs): """Create a new phylogeny containing just this clade.""" phy = Phylogeny(root=self, date=self.date) phy.__dict__.update(kwargs) return phy # Shortcuts for list attributes that are usually only 1 item def _get_confidence(self): if len(self.confidences) == 0: return None if len(self.confidences) > 1: raise AttributeError("more than 1 confidence value available; " "use Clade.confidences") return self.confidences[0] def _set_confidence(self, value): if isinstance(value, float) or isinstance(value, int): value = Confidence(value) elif not isinstance(value, Confidence): raise ValueError("value must be a number or Confidence instance") if len(self.confidences) == 0: self.confidences.append(value) elif len(self.confidences) == 1: self.confidences[0] = value else: raise ValueError("multiple confidence values already exist; " "use Phylogeny.confidences instead") confidence = property(_get_confidence, _set_confidence) def _get_taxonomy(self): if len(self.taxonomies) == 0: return None if len(self.taxonomies) > 1: raise AttributeError("more than 1 taxonomy value available; " "use Clade.taxonomies") return self.taxonomies[0] def _set_taxonomy(self, value): if not isinstance(value, Taxonomy): raise ValueError("assigned value must be a Taxonomy instance") if len(self.taxonomies) == 0: self.taxonomies.append(value) elif len(self.taxonomies) == 1: self.taxonomies[0] = value else: raise ValueError("multiple taxonomy values already exist; " "use Phylogeny.taxonomies instead") taxonomy = property(_get_taxonomy, _set_taxonomy) # Syntax sugar for setting the branch color def _get_color(self): return self._color def _set_color(self, arg): if arg is None or isinstance(arg, BranchColor): self._color = arg elif isinstance(arg, basestring): if arg in BranchColor.color_names: # Known color name self._color = BranchColor.from_name(arg) elif arg.startswith('#') and len(arg) == 7: # HTML-style hex string self._color = BranchColor.from_hex(arg) else: raise ValueError("invalid color string %s" % arg) elif hasattr(arg, '__iter__') and len(arg) == 3: # RGB triplet self._color = BranchColor(*arg) else: raise ValueError("invalid color value %s" % arg) color = property(_get_color, _set_color, doc="Branch color.") # PhyloXML-specific complex types class Accession(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'. """ def __init__(self, value, source): self.value = value self.source = source def __str__(self): """Show the class name and an identifying attribute.""" return '%s:%s' % (self.source, self.value) class Annotation(PhyloElement): """The annotation of a molecular sequence. It is recommended to annotate by using the optional 'ref' attribute (some examples of acceptable values for the ref attribute: 'GO:0008270', 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1'). @type ref: str @param source: plain-text source for this annotation @param evidence: describe evidence as free text (e.g. 'experimental') @type type: str @param desc: free text description @param confidence: state the type and value of support (type Confidence) @param properties: list of typed and referenced annotations from external resources @type uri: Uri """ re_ref = re.compile(r'[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+') def __init__(self, # Attributes ref=None, source=None, evidence=None, type=None, # Child nodes desc=None, confidence=None, uri=None, # Collection properties=None): _check_str(ref, self.re_ref.match) self.ref = ref self.source = source self.evidence = evidence self.type = type self.desc = desc self.confidence = confidence self.uri = uri self.properties = properties or [] class BinaryCharacters(PhyloElement): """The names and/or counts of binary characters present, gained, and lost at the root of a clade. """ def __init__(self, # Attributes type=None, gained_count=None, lost_count=None, present_count=None, absent_count=None, # Child nodes (flattened into collections) gained=None, lost=None, present=None, absent=None): self.type=type self.gained_count=gained_count self.lost_count=lost_count self.present_count=present_count self.absent_count=absent_count self.gained=gained or [] self.lost=lost or [] self.present=present or [] self.absent=absent or [] class BranchColor(PhyloElement): """Indicates the color of a clade when rendered graphically. The color should be interpreted by client code (e.g. visualization programs) as applying to the whole clade, unless overwritten by the color(s) of sub-clades. Color values must be integers from 0 to 255. """ color_names = { 'red': (255, 0, 0), 'r': (255, 0, 0), 'yellow': (255, 255, 0), 'y': (255, 255, 0), 'green': ( 0, 128, 0), 'g': ( 0, 128, 0), 'cyan': ( 0, 255, 255), 'c': ( 0, 255, 255), 'blue': ( 0, 0, 255), 'b': ( 0, 0, 255), 'magenta': (255, 0, 255), 'm': (255, 0, 255), 'black': ( 0, 0, 0), 'k': ( 0, 0, 0), 'white': (255, 255, 255), 'w': (255, 255, 255), # Names standardized in HTML/CSS spec # http://w3schools.com/html/html_colornames.asp 'maroon': (128, 0, 0), 'olive': (128, 128, 0), 'lime': ( 0, 255, 0), 'aqua': ( 0, 255, 255), 'teal': ( 0, 128, 128), 'navy': ( 0, 0, 128), 'fuchsia': (255, 0, 255), 'purple': (128, 0, 128), 'silver': (192, 192, 192), 'gray': (128, 128, 128), # More definitions from matplotlib/gcolor2 'grey': (128, 128, 128), 'pink': (255, 192, 203), 'salmon': (250, 128, 114), 'orange': (255, 165, 0), 'gold': (255, 215, 0), 'tan': (210, 180, 140), 'brown': (165, 42, 42), } def __init__(self, red, green, blue): for color in (red, green, blue): assert (isinstance(color, int) and 0 <= color <= 255 ), "Color values must be integers between 0 and 255." self.red = red self.green = green self.blue = blue @classmethod def from_hex(cls, hexstr): """Construct a BranchColor object from a hexadecimal string. The string format is the same style used in HTML and CSS, such as '#FF8000' for an RGB value of (255, 128, 0). """ assert (isinstance(hexstr, basestring) and hexstr.startswith('#') and len(hexstr) == 7 ), "need a 24-bit hexadecimal string, e.g. #000000" def unpack(cc): return int('0x'+cc, base=16) RGB = hexstr[1:3], hexstr[3:5], hexstr[5:] return cls(*map(unpack, RGB)) @classmethod def from_name(cls, colorname): """Construct a BranchColor object by the color's name.""" return cls(*cls.color_names[colorname]) def to_hex(self): """Return a 24-bit hexadecimal RGB representation of this color. The returned string is suitable for use in HTML/CSS, as a color parameter in matplotlib, and perhaps other situations. Example: >>> bc = BranchColor(12, 200, 100) >>> bc.to_hex() '#0cc864' """ return '#' + hex( self.red * (16**4) + self.green * (16**2) + self.blue)[2:].zfill(6) def to_rgb(self): """Return a tuple of RGB values (0 to 255) representing this color. Example: >>> bc = BranchColor(255, 165, 0) >>> bc.to_rgb() (255, 165, 0) """ return (self.red, self.green, self.blue) def __repr__(self): """Preserve the standard RGB order when representing this object.""" return (u'%s(red=%d, green=%d, blue=%d)' % (self.__class__.__name__, self.red, self.green, self.blue)) def __str__(self): """Show the color's RGB values.""" return "(%d, %d, %d)" % (self.red, self.green, self.blue) class CladeRelation(PhyloElement): """Expresses a typed relationship between two clades. For example, this could be used to describe multiple parents of a clade. @type id_ref_0: str @type id_ref_1: str @type distance: str @type type: str @type confidence: Confidence """ def __init__(self, type, id_ref_0, id_ref_1, distance=None, confidence=None): self.distance = distance self.type = type self.id_ref_0 = id_ref_0 self.id_ref_1 = id_ref_1 self.confidence = confidence class Confidence(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'). @type value: float @type type: str """ def __init__(self, value, type='unknown'): self.value = value self.type = type def __float__(self): return float(self.value) def __int__(self): return int(self.value) class Date(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. @param unit: type of numerical value (e.g. 'mya' for 'million years ago') @type value: float @param desc: plain-text description of the date @param minimum: lower bound on the date value @param maximum: upper bound on the date value """ def __init__(self, value=None, unit=None, desc=None, minimum=None, maximum=None): self.value = value self.unit = unit self.desc = desc self.minimum = minimum self.maximum = maximum def __str__(self): """Show the class name and the human-readable date.""" if self.unit and self.value is not None: return '%s %s' % (self.value, self.unit) if self.desc is not None: return self.desc return self.__class__.__name__ class Distribution(PhyloElement): """Geographic distribution of the items of a clade (species, sequences). Intended for phylogeographic applications. The location can be described either by free text in the 'desc' element and/or by the coordinates of one or more 'Points' (similar to the 'Point' element in Google's KML format) or by 'Polygons'. """ def __init__(self, desc=None, points=None, polygons=None): self.desc = desc self.points = points or [] self.polygons = polygons or [] class DomainArchitecture(PhyloElement): """Domain architecture of a protein. @param length: total length of the protein sequence (type int) @param domains: list of ProteinDomain objects """ def __init__(self, length=None, domains=None): self.length = length self.domains = domains class Events(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 = set(('transfer', 'fusion', 'speciation_or_duplication', 'other', 'mixed', 'unassigned')) def __init__(self, type=None, duplications=None, speciations=None, losses=None, confidence=None): _check_str(type, self.ok_type.__contains__) self.type = type self.duplications = duplications self.speciations = speciations self.losses = losses self.confidence = confidence def items(self): return [(k, v) for k, v in self.__dict__.iteritems() if v is not None] def keys(self): return [k for k, v in self.__dict__.iteritems() if v is not None] def values(self): return [v for v in self.__dict__.itervalues() if v is not None] # XXX Backwards compatibility shims -- remove in Biopython 1.56 def iteritems(self): warnings.warn("use items() instead.""", DeprecationWarning, stacklevel=2) return iter(self.items()) def iterkeys(self): warnings.warn("use keys() instead.""", DeprecationWarning, stacklevel=2) return iter(self.keys()) def itervalues(self): warnings.warn("use values() instead.""", DeprecationWarning, stacklevel=2) return iter(self.values()) def __len__(self): return len(self.values()) def __getitem__(self, key): if not hasattr(self, key): raise KeyError(key) val = getattr(self, key) if val is None: raise KeyError("%s has not been set in this object" % repr(key)) return val def __setitem__(self, key, val): setattr(self, key, val) def __delitem__(self, key): setattr(self, key, None) def __iter__(self): return iter(self.keys()) def __contains__(self, key): return (hasattr(self, key) and getattr(self, key) is not None) class Id(PhyloElement): """A general-purpose identifier element. Allows to indicate the provider (or authority) of an identifier, e.g. NCBI, along with the value itself. """ def __init__(self, value, provider=None): self.value = value self.provider = provider def __str__(self): if self.provider is not None: return '%s:%s' % (self.provider, self.value) return self.value class MolSeq(PhyloElement): """Store a molecular sequence. @param value: the sequence, as a string @param is_aligned: True is mol_seq is aligned (usu. meaning gaps are introduced and all aligned seqs are the same length) """ re_value = re.compile(r'[a-zA-Z\.\-\?\*_]+') def __init__(self, value, is_aligned=None): _check_str(value, self.re_value.match) self.value = value self.is_aligned = is_aligned def __str__(self): return self.value class Point(PhyloElement): """Geographic coordinates of a point, with an optional altitude. Used by element 'Distribution'. @param geodetic_datum: indicate the geodetic datum (also called 'map datum'). For example, Google's KML uses 'WGS84'. (required) @param lat: latitude @param long: longitude @param alt: altitude @param alt_unit: unit for the altitude (e.g. 'meter') """ def __init__(self, geodetic_datum, lat, long, alt=None, alt_unit=None): self.geodetic_datum = geodetic_datum self.lat = lat self.long = long self.alt = alt self.alt_unit = alt_unit class Polygon(PhyloElement): """A polygon defined by a list of 'Points' (used by element 'Distribution'). @param points: list of 3 or more points representing vertices. """ def __init__(self, points=None): self.points = points or [] def __str__(self): return '%s([%s])' % (self.__class__.__name__, ',\n'.join(map(str, self.points))) class Property(PhyloElement): """A typed and referenced property from an external resources. Can be attached to 'Phylogeny', 'Clade', and 'Annotation' objects. @param ref: reference to an external resource, e.g. "NOAA:depth" @param unit: the unit of the property, e.g. "METRIC:m" (optional) @param datatype: indicates the type of a property and is limited to xsd-datatypes (e.g. 'xsd:string', 'xsd:boolean', 'xsd:integer', 'xsd:decimal', 'xsd:float', 'xsd:double', 'xsd:date', 'xsd:anyURI'). @param applies_to: 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'). @param id_ref: allows to attached a property specifically to one element (on the xml-level). (optional) @type value: str """ re_ref = re.compile(r'[a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+') ok_applies_to = set(('phylogeny', 'clade', 'node', 'annotation', 'parent_branch', 'other')) ok_datatype = set(('xsd:string', 'xsd:boolean', 'xsd:decimal', 'xsd:float', 'xsd:double', 'xsd:duration', 'xsd:dateTime', 'xsd:time', 'xsd:date', 'xsd:gYearMonth', 'xsd:gYear', 'xsd:gMonthDay', 'xsd:gDay', 'xsd:gMonth', 'xsd:hexBinary', 'xsd:base64Binary', 'xsd:anyURI', 'xsd:normalizedString', 'xsd:token', 'xsd:integer', 'xsd:nonPositiveInteger', 'xsd:negativeInteger', 'xsd:long', 'xsd:int', 'xsd:short', 'xsd:byte', 'xsd:nonNegativeInteger', 'xsd:unsignedLong', 'xsd:unsignedInt', 'xsd:unsignedShort', 'xsd:unsignedByte', 'xsd:positiveInteger')) def __init__(self, value, ref, applies_to, datatype, unit=None, id_ref=None): _check_str(ref, self.re_ref.match) _check_str(applies_to, self.ok_applies_to.__contains__) _check_str(datatype, self.ok_datatype.__contains__) _check_str(unit, self.re_ref.match) self.unit = unit self.id_ref = id_ref self.value = value self.ref = ref self.applies_to = applies_to self.datatype = datatype class ProteinDomain(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. @param start: start of the domain on the sequence, using 0-based indexing @type start: non-negative integer @param end: end of the domain on the sequence @type end: non-negative integer @param confidence: can be used to store e.g. E-values. (type float) @param id: unique identifier/name """ # TODO: confirm that 'start' counts from 1, not 0 def __init__(self, value, start, end, confidence=None, id=None): self.value = value self.start = start self.end = end self.confidence = confidence self.id = id @classmethod def from_seqfeature(cls, feat): return ProteinDomain(feat.id, feat.location.nofuzzy_start, feat.location.nofuzzy_end, confidence=feat.qualifiers.get('confidence')) def to_seqfeature(self): feat = SeqFeature(location=FeatureLocation(self.start, self.end), id=self.value) if hasattr(self, 'confidence'): feat.qualifiers['confidence'] = self.confidence return feat class Reference(PhyloElement): """Literature reference for a clade. It is recommended to use the 'doi' attribute instead of the free text 'desc' element whenever possible. """ re_doi = re.compile(r'[a-zA-Z0-9_\.]+/[a-zA-Z0-9_\.]+') def __init__(self, doi=None, desc=None): _check_str(doi, self.re_doi.match) self.doi = doi self.desc = desc class Sequence(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. @param type: type of sequence ('dna', 'rna', or 'protein'). @type id_ref: str @type id_source: str @param symbol: short symbol of the sequence, e.g. 'ACTM' (max. 10 chars) @type accession: Accession @param name: full name of the sequence, e.g. 'muscle Actin' @param location: location of a sequence on a genome/chromosome. @type mol_seq: MolSeq @type uri: Uri @param annotations: list of Annotation objects @param domain_architecture: protein domains on this sequence (type DomainArchitecture) @param other: list of non-phyloXML elements (type Other) """ alphabets = {'dna': Alphabet.generic_dna, 'rna': Alphabet.generic_rna, 'protein': Alphabet.generic_protein} re_symbol = re.compile(r'\S{1,10}') def __init__(self, # Attributes type=None, id_ref=None, id_source=None, # Child nodes symbol=None, accession=None, name=None, location=None, mol_seq=None, uri=None, domain_architecture=None, # Collections annotations=None, other=None, ): _check_str(type, self.alphabets.__contains__) _check_str(symbol, self.re_symbol.match) self.type = type self.id_ref = id_ref self.id_source = id_source self.symbol = symbol self.accession = accession self.name = name self.location = location self.mol_seq = mol_seq self.uri = uri self.domain_architecture = domain_architecture self.annotations = annotations or [] self.other = other or [] @classmethod def from_seqrecord(cls, record, is_aligned=None): """Create a new PhyloXML Sequence from a SeqRecord object.""" if is_aligned == None: is_aligned = isinstance(record.seq.alphabet, Alphabet.Gapped) params = { 'accession': Accession(record.id, ''), 'symbol': record.name, 'name': record.description, 'mol_seq': MolSeq(str(record.seq), is_aligned), } if isinstance(record.seq.alphabet, Alphabet.DNAAlphabet): params['type'] = 'dna' elif isinstance(record.seq.alphabet, Alphabet.RNAAlphabet): params['type'] = 'rna' elif isinstance(record.seq.alphabet, Alphabet.ProteinAlphabet): params['type'] = 'protein' # Unpack record.annotations for key in ('id_ref', 'id_source', 'location'): if key in record.annotations: params[key] = record.annotations[key] if isinstance(record.annotations.get('uri'), dict): params['uri'] = Uri(**record.annotations['uri']) # Build a Sequence.annotation object if record.annotations.get('annotations'): params['annotations'] = [] for annot in record.annotations['annotations']: ann_args = {} for key in ('ref', 'source', 'evidence', 'type', 'desc'): if key in annot: ann_args[key] = annot[key] if isinstance(annot.get('confidence'), list): ann_args['confidence'] = Confidence( *annot['confidence']) if isinstance(annot.get('properties'), list): ann_args['properties'] = [Property(**prop) for prop in annot['properties'] if isinstance(prop, dict)] params['annotations'].append(Annotation(**ann_args)) # Unpack record.features if record.features: params['domain_architecture'] = DomainArchitecture( length=len(record.seq), domains=[ProteinDomain.from_seqfeature(feat) for feat in record.features]) return Sequence(**params) def to_seqrecord(self): """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], } """ def clean_dict(dct): """Remove None-valued items from a dictionary.""" return dict((key, val) for key, val in dct.iteritems() if val is not None) seqrec = SeqRecord(Seq(self.mol_seq.value, self.get_alphabet()), **clean_dict({ 'id': str(self.accession), 'name': self.symbol, 'description': self.name, # 'dbxrefs': None, })) if self.domain_architecture: seqrec.features = [dom.to_seqfeature() for dom in self.domain_architecture.domains] # Sequence attributes with no SeqRecord equivalent seqrec.annotations = clean_dict({ 'id_ref': self.id_ref, 'id_source': self.id_source, 'location': self.location, 'uri': self.uri and clean_dict({ 'value': self.uri.value, 'desc': self.uri.desc, 'type': self.uri.type, }), 'annotations': self.annotations and [ clean_dict({ 'ref': ann.ref, 'source': ann.source, 'evidence': ann.evidence, 'type': ann.type, 'confidence': ann.confidence and [ ann.confidence.value, ann.confidence.type], 'properties': [clean_dict({ '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], }) return seqrec def get_alphabet(self): alph = self.alphabets.get(self.type, Alphabet.generic_alphabet) if self.mol_seq and self.mol_seq.is_aligned: return Alphabet.Gapped(alph) return alph class SequenceRelation(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'). @param id_ref_0: first sequence reference identifier @param id_ref_1: second sequence reference identifier @param distance: distance between the two sequences (type float) @param type: describe the type of relationship @type confidence: Confidence """ ok_type = set(('orthology', 'one_to_one_orthology', 'super_orthology', 'paralogy', 'ultra_paralogy', 'xenology', 'unknown', 'other')) def __init__(self, type, id_ref_0, id_ref_1, distance=None, confidence=None): _check_str(type, self.ok_type.__contains__) self.distance = distance self.type = type self.id_ref_0 = id_ref_0 self.id_ref_1 = id_ref_1 self.confidence = confidence class Taxonomy(PhyloElement): """Describe taxonomic information for a clade. @param id_source: link other elements to a taxonomy (on the XML level) @param id: unique identifier of a taxon, e.g. Id('6500', provider='ncbi_taxonomy') for the California sea hare @param code: store UniProt/Swiss-Prot style organism codes, e.g. 'APLCA' for the California sea hare 'Aplysia californica' (restricted string) @param scientific_name: the standard scientific name for this organism, e.g. 'Aplysia californica' for the California sea hare @param authority: keep the authority, such as 'J. G. Cooper, 1863', associated with the 'scientific_name' @param common_names: list of common names for this organism @param synonyms: ??? @param rank: taxonomic rank (restricted string) @type uri: Uri @param other: list of non-phyloXML elements (type Other) """ re_code = re.compile(r'[a-zA-Z0-9_]{2,10}') ok_rank = set(('domain', 'kingdom', 'subkingdom', 'branch', 'infrakingdom', 'superphylum', 'phylum', 'subphylum', 'infraphylum', 'microphylum', 'superdivision', 'division', 'subdivision', 'infradivision', 'superclass', 'class', 'subclass', 'infraclass', 'superlegion', 'legion', 'sublegion', 'infralegion', 'supercohort', 'cohort', 'subcohort', 'infracohort', 'superorder', 'order', 'suborder', 'superfamily', 'family', 'subfamily', 'supertribe', 'tribe', 'subtribe', 'infratribe', 'genus', 'subgenus', 'superspecies', 'species', 'subspecies', 'variety', 'subvariety', 'form', 'subform', 'cultivar', 'unknown', 'other')) def __init__(self, # Attributes id_source=None, # Child nodes id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, # Collections common_names=None, synonyms=None, other=None, ): _check_str(code, self.re_code.match) _check_str(rank, self.ok_rank.__contains__) self.id_source = id_source self.id = id self.code = code self.scientific_name = scientific_name self.authority = authority self.rank = rank self.uri = uri self.common_names = common_names or [] self.synonyms = synonyms or [] self.other = other or [] def __str__(self): """Show the class name and an identifying attribute.""" if self.code is not None: return self.code if self.scientific_name is not None: return self.scientific_name if self.rank is not None: return self.rank if self.id is not None: return str(self.id) return self.__class__.__name__ class Uri(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'). """ def __init__(self, value, desc=None, type=None): self.value = value self.desc = desc self.type = type def __str__(self): if self.value: return self.value return repr(self)