o Rŀg@s@dZddlZddlZddlmZddlmZddlmZddlm Z ddl m Z ddl m Z dd l mZdd lmZGd d d eZd dZGddde jZGdddeZGdddeZGdddee jZGdddee jZGdddee jZGdddeZGdddeZGdd d eZGd!d"d"eZGd#d$d$eeZ Gd%d&d&eZ!Gd'd(d(eZ"Gd)d*d*eZ#Gd+d,d,eZ$Gd-d.d.eZ%Gd/d0d0eZ&Gd1d2d2eZ'Gd3d4d4eZ(Gd5d6d6eZ)Gd7d8d8eZ*Gd9d:d:eZ+Gd;d<dd>eZ-Gd?d@d@eZ.GdAdBdBeZ/dS)CzClasses corresponding to phyloXML elements. See Also -------- Official specification: http://phyloxml.org/ Journal article: Han and Zmasek (2009), https://doi.org/10.1186/1471-2105-10-356 N)BiopythonWarning) Alignment)MultipleSeqAlignment)BaseTree)Seq) SeqFeature)SimpleLocation) SeqRecordc@eZdZdZdS)PhyloXMLWarningz;Warning for non-compliance with the phyloXML specification.N__name__ __module__ __qualname____doc__rrF/var/www/html/myenv/lib/python3.10/site-packages/Bio/Phylo/PhyloXML.pyr r cCs4|dur||stjd|dtdddSdSdS)zFCheck a string using testfunc, and warn if there's no match (PRIVATE).NzString z doesn't match the given regexp) stacklevel)warningswarnr )texttestfuncrrr _check_str$s  rc@r ) PhyloElementz$Base class for all PhyloXML objects.Nr rrrrr1rrc@s:eZdZdZd ddZddZddZd d Zd d ZdS)PhyloxmlavRoot node of the PhyloXML document. Contains an arbitrary number of Phylogeny elements, possibly followed by elements from other namespaces. :Parameters: attributes : dict (XML namespace definitions) phylogenies : list The phylogenetic trees other : list Arbitrary non-phyloXML elements, if any NcCs6dddd|_|r|j||pg|_|pg|_dS)z*Initialize parameters for PhyloXML object.z)http://www.w3.org/2001/XMLSchema-instancezhttp://www.phyloxml.orgzAhttp://www.phyloxml.org http://www.phyloxml.org/1.10/phyloxml.xsd)z xmlns:xsixmlnszxsi:schemaLocationN) attributesupdate phylogeniesother)selfrr r!rrr__init__Es  zPhyloxml.__init__cCsbt|ttfr |j|St|tstdt|d|jD] }|j|kr)|Sqtd|)z!Get a phylogeny by index or name.z can't use z as an indexzno phylogeny found with name ) isinstanceintslicer strKeyErrortypename)r"indextreerrr __getitem__Rs    zPhyloxml.__getitem__cC t|jS)z6Iterate through the phylogenetic trees in this object.)iterr r"rrr__iter__^ zPhyloxml.__iter__cCr.)z7Return the number of phylogenetic trees in this object.)lenr r0rrr__len__br2zPhyloxml.__len__cCd|jjdtt|jfS)z)Return name of phylogenies in the object.%s([%s]), ) __class__r joinmapr'r r0rrr__str__fszPhyloxml.__str__NN) r rrrr#r-r1r4r;rrrrr5s    rc@"eZdZdZdddZddZdS)OtheraContainer 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: tag : string local tag for the XML node namespace : string XML namespace for the node -- should not be the default phyloXML namespace. attributes : dict of strings attributes on the XML node value : string text contained directly within this XML node children : list child nodes, if any (also ``Other`` instances) NcCs*||_||_|p i|_||_|pg|_dS)z,Initialize values for non-phyloXML elements.N)tag namespacervaluechildren)r"r?r@rrArBrrrr#s  zOther.__init__cCr.)z5Iterate through the children of this object (if any).)r/rBr0rrrr1r2zOther.__iter__)NNNN)r rrrr#r1rrrrr>n  r>c@seZdZdZ              dddZeddZedd Zd d Zd d Z ddZ e ddZ ddZ ddZddZe e eeZdS) PhylogenyaA phylogenetic tree. :Parameters: root : Clade the root node/clade of this tree rooted : bool True if this tree is rooted rerootable : bool True if this tree is rerootable branch_length_unit : string unit for branch_length values on clades name : string identifier for this tree, not required to be unique id : Id unique identifier for this tree description : string plain-text description date : Date date for the root node of this tree confidences : list Confidence objects for this tree clade_relations : list CladeRelation objects sequence_relations : list SequenceRelation objects properties : list Property objects other : list non-phyloXML elements (type ``Other``) NTcCszt|tsJ||_||_||_||_||_||_||_||_ | |_ | p%g|_ | p*g|_ | p/g|_ | p4g|_|p9g|_dS)z/Initialize values for phylogenetic tree object.N)r$boolrootrooted rerootablebranch_length_unitr)r*id descriptiondate confidencesclade_relationssequence_relations propertiesr!)r"rFrGrHrIr)r*rJrKrLrMrNrOrPr!rrrr#s    zPhylogeny.__init__cKsD|t|j|j|j|jdurtt|jpdd}|j ||S)zCreate a new Phylogeny given a Tree (from Newick/Nexus or BaseTree). 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Overrides the ``BaseTree`` method. rr0rrr as_phyloxmlszPhylogeny.as_phyloxmlcKst||gdS)z.is_aligned_seqpreorderTcss|]}|VqdSN) to_seqrecord).0seqrrr sz)Phylogeny.to_alignment..)_filter_searchr)r"rfseqsrecordsrrr to_alignmentszPhylogeny.to_alignmentc Csdd}||dd}g}g}|D]}|}|t|j||q|r>t|\}}t||D] \} }t| |_q3nd}t||S)zFConstruct an Alignment object from the aligned sequences in this tree.cSr^r_r`rdrrrrfrgz+Phylogeny.alignment..is_aligned_seqrhTN) rnrjappendbytesrlrparse_printed_alignmentzipr) r"rfrorplinesrlrecord sequences coordinatessequencerrr alignments   zPhylogeny.alignmentcC2t|jdkr dSt|jdkrtd|jdS)zEquivalent to self.confidences[0] if there is only 1 value (PRIVATE). See Also: ``Clade.confidence``, ``Clade.taxonomy`` rNzAmore than 1 confidence value available; use Phylogeny.confidencesr3rMAttributeErrorr0rrr_get_confidences zPhylogeny._get_confidencecCs~|dur g|_dSt|ttfrt|}n t|tstdt|jdkr-|j|dSt|jdkr;||jd<dStd)N-value must be a number or Confidence instancerr}Kmultiple confidence values already exist; use Phylogeny.confidences insteadrMr$floatr% Confidence ValueErrorr3rrr"rArrr_set_confidence*s  zPhylogeny._set_confidencecCs g|_dSrirMr0rrr_del_confidence=s zPhylogeny._del_confidence)NTNNNNNNNNNNNN)r rrrr# classmethodrXrRr[r\rqpropertyr{rrr confidencerrrrrDs<" $   rDc@seZdZdZ                 dddZeddZddZd d Zd d Z d dZ e ee e Z ddZ ddZe e eZdS)rQaDescribes 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) name : string short label for this clade confidences : list of Confidence objects used to indicate the support for a clade/parent branch. width : float branch width for this clade (including branch from parent) color : BranchColor color used for graphical display of this clade node_id unique identifier for the root node of this clade taxonomies : list Taxonomy objects sequences : list Sequence objects events : Events describe such events as gene-duplications at the root node/parent branch of this clade binary_characters : BinaryCharacters binary characters distributions : list of Distribution objects distribution(s) of this clade date : Date a date for the root node of this clade references : list Reference objects properties : list Property objects clades : list Clade objects Sub-clades other : list of Other objects non-phyloXML objects NcCs||_||_||_||_||_||_||_||_| |_| pg|_ | p#g|_ | p(g|_ | p-g|_ |p2g|_ |p7g|_|psz$Clade.from_clade..N) rr*rrrr BranchColorredgreenbluerTr)rUrZrV new_claderrrrRs zClade.from_cladecKst||jd}|j||S)z2Create a new phylogeny containing just this clade.)rFrL)rDrLrTr)r"rVrWrrrrYs zClade.to_phylogenycCr|)z#Return confidence values (PRIVATE).rNr}z=more than 1 confidence value available; use Clade.confidencesr~r0rrrr zClade._get_confidencecCs~|dur g|_dSt|ttfrt|}n t|tstdt|jdkr-|j|dSt|jdkr;||jd<dStd)z#Set the confidence value (PRIVATE).Nrrr}rrrrrrrs  zClade._set_confidencecCs g|_dS)z$Delete confidences values (PRIVATE).Nrr0rrrrr2zClade._del_confidencecCr|)z*Get taxonomy list for the clade (PRIVATE).rNr}z:more than 1 taxonomy value available; use Clade.taxonomies)r3rrr0rrr _get_taxonomyrzClade._get_taxonomycCsTt|ts tdt|jdkr|j|dSt|jdkr&||jd<dStd)z'Set a taxonomy for the clade (PRIVATE).z*assigned value must be a Taxonomy instancerr}zHmultiple taxonomy values already exist; use Phylogeny.taxonomies insteadN)r$Taxonomyrr3rrrrrrr _set_taxonomys zClade._set_taxonomy)NNNNNNNNNNNNNNNNN)r rrrr#rrRrYrrrrrrrtaxonomyrrrrrQCs<3 *    rQc@seZdZdZddZdS)rzManage Tree branch's color.cOstjj|g|Ri|dS)z1Initialize parameters for the BranchColor object.N)rrr#)r"argsrVrrrr#zBranchColor.__init__Nr rrrr#rrrrrs rc@s eZdZdZddZddZdS) AccessionzCaptures the local part in a sequence identifier. Example: In ``UniProtKB:P17304``, the Accession instance attribute ``value`` is 'P17304' and the ``source`` attribute is 'UniProtKB'. cC||_||_dS)z&Initialize value for Accession object.N)rAsource)r"rArrrrr#  zAccession.__init__cCs|jd|jS)1Show the class name and an identifying attribute.:)rrAr0rrrr;zAccession.__str__Nr rrrr#r;rrrrrs rc@s4eZdZdZedZ        dddZdS) AnnotationaThe annotation of a molecular sequence. It is recommended to annotate by using the optional 'ref' attribute. :Parameters: ref : string reference string, e.g. 'GO:0008270', 'KEGG:Tetrachloroethene degradation', 'EC:1.1.1.1' source : string plain-text source for this annotation evidence : str describe evidence as free text (e.g. 'experimental') desc : string free text description confidence : Confidence state the type and value of support (type Confidence) properties : list typed and referenced annotations from external resources uri : Uri link ![a-zA-Z0-9_]+:[a-zA-Z0-9_\.\-\s]+Nc CsFt||jj||_||_||_||_||_||_||_ |pg|_ dS)z+Initialize value for the Annotation object.N) rre_refmatchrefrevidencer)descrurirP) r"rrrr)rrrrPrrrr#0szAnnotation.__init__)NNNNNNNN)r rrrrecompilerr#rrrrrs rc@s,eZdZdZ         dddZdS)BinaryCharacterszBinary 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. Nc CsJ||_||_||_||_||_|pg|_|pg|_|pg|_| p!g|_dS)z2Initialize values for the BinaryCharacters object.N) r) gained_count lost_count present_count absent_countgainedlostpresentabsent) r"r)rrrrrrrrrrrr#Qs   zBinaryCharacters.__init__) NNNNNNNNNrrrrrrJs rc@eZdZdZdddZdS) CladeRelationaExpresses 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 NcCs"||_||_||_||_||_dS)z/Initialize values for the CladeRelation object.N)distancer)id_ref_0id_ref_1rr"r)rrrrrrrr#x  zCladeRelation.__init__r<rrrrrrks rcs.eZdZdZdfdd ZeddZZS)raUA 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: value : float confidence value type : string label for the type of confidence, e.g. 'bootstrap' unknowncst||}||_|S)zHCreate and return a Confidence object with the specified value and type.)super__new__r))rUrAr)objr8rrrszConfidence.__new__cCst|S)z0Return the float value of the Confidence object.)rr0rrrrAszConfidence.value)r)r rrrrrrA __classcell__rrrrrs  rc@r=)DateagA 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: unit : string type of numerical value (e.g. 'mya' for 'million years ago') value : float the date value desc : string plain-text description of the date minimum : float lower bound on the date value maximum : float upper bound on the date value NcC"||_||_||_||_||_dS)z%Initialize values of the Date object.N)rAunitrminimummaximum)r"rArrrrrrrr#rz Date.__init__cCs:|jr|jdur|jd|jS|jdur|jS|jjS)z0Show the class name and the human-readable date.N )rrArr8r r0rrrr;s  z Date.__str__NNNNNrrrrrrrCrc@r) DistributionaGeographic distribution of the items of a clade (species, sequences). Intended for phylogeographic applications. :Parameters: desc : string free-text description of the location points : list of ``Point`` objects coordinates (similar to the 'Point' element in Google's KML format) polygons : list of ``Polygon`` objects coordinate sets defining geographic regions NcCs||_|pg|_|p g|_dS)z)Initialize values of Distribution object.N)rpointspolygons)r"rrrrrrr#s zDistribution.__init__)NNNrrrrrrsrc@r)DomainArchitecturezDomain architecture of a protein. :Parameters: length : int total length of the protein sequence domains : list ProteinDomain objects the domains within this protein NcCr)z3Initialize values of the DomainArchitecture object.Nlengthdomains)r"rrrrrr#rzDomainArchitecture.__init__r<rrrrrrs rc@steZdZdZhdZ     dddZddZdd Zd d Zd d Z ddZ ddZ ddZ ddZ ddZdS)Eventsa&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. >mixedr!fusiontransfer unassignedspeciation_or_duplicationNcCs0t||jj||_||_||_||_||_dS)z'Initialize values of the Events object.N)rok_type __contains__r) duplications speciationslossesr)r"r)rrrrrrrr#s   zEvents.__init__cCdd|jDS)zReturn Event's items.cSs g|] \}}|dur||fqSrirrkkvrrrr s z Events.items..rTitemsr0rrrr z Events.itemscCr)zReturn Event's keys.cSsg|] \}}|dur|qSrirrrrrrszEvents.keys..rr0rrrkeys rz Events.keyscCr)z6Return values from a key-value pair in an Events dict.cSsg|]}|dur|qSrir)rkrrrrrsz!Events.values..)rTvaluesr0rrrrrz Events.valuescC t|S)zReturn number of Events.)r3rr0rrrr4s zEvents.__len__cCsBzt||}Wn tyt|dw|durt|d|S)z&Get value of Event with the given key.Nz has not been set in this object)getattrrr(r"keyvalrrrr-s  zEvents.__getitem__cCst|||dS)zAdd item to Event dict.Nsetattrrrrr __setitem__$zEvents.__setitem__cCst||ddS)zDelete Event with given key.Nrr"rrrr __delitem__(rzEvents.__delitem__cCr)z/Iterate over the keys present in a Events dict.)r/rr0rrrr1,s zEvents.__iter__cCs&zt||duWStyYdSw)z'Return True if Event dict contains key.NF)rrrrrrr0s  zEvents.__contains__r)r rrrrr#rrrr4r-rrr1rrrrrrs$    rc@r=)rSzA general-purpose identifier element. Allows to indicate the provider (or authority) of an identifier, e.g. NCBI, along with the value itself. NcCr)z,Initialize values for the identifier object.N)rAprovider)r"rArrrrr#?rz Id.__init__cCs"|jdur|jd|jS|jS)zReturn identifier as a string.Nr)rrAr0rrrr;Ds z Id.__str__rirrrrrrS8s  rSc@s,eZdZdZedZdddZddZdS) MolSeqaStore a molecular sequence. :Parameters: value : string the sequence itself is_aligned : bool True if this sequence is aligned with the others (usually meaning all aligned seqs are the same length and gaps may be present) z[a-zA-Z\.\-\?\*_]+NcCt||jj||_||_dS)z,Initialize parameters for the MolSeq object.N)rre_valuerrArc)r"rArcrrrr#Y zMolSeq.__init__cCs|jS)z2Return the value of the Molecular Sequence object.)rAr0rrrr;_szMolSeq.__str__ri) r rrrrrrr#r;rrrrrKs   rc@r)PointaGeographic coordinates of a point, with an optional altitude. Used by element 'Distribution'. :Parameters: geodetic_datum : string, required the geodetic datum (also called 'map datum'). For example, Google's KML uses 'WGS84'. lat : numeric latitude long : numeric longitude alt : numeric altitude alt_unit : string unit for the altitude (e.g. 'meter') NcCr)z&Initialize value for the Point object.N)geodetic_datumlatlongaltalt_unit)r"rrrrrrrrr#xrzPoint.__init__r<rrrrrrdsrc@r=)PolygonzA polygon defined by a list of 'Points' (used by element 'Distribution'). :param points: list of 3 or more points representing vertices. NcCs|pg|_dS)z(Initialize value for the Polygon object.N)r)r"rrrrr#r]zPolygon.__init__cCr5)z"Return list of points as a string.r6r7)r8r r9r:r'rr0rrrr;rzPolygon.__str__rirrrrrr s  r c@s4eZdZdZedZhdZhdZdddZ dS) PropertyaA typed and referenced property from an external resources. Can be attached to ``Phylogeny``, ``Clade``, and ``Annotation`` objects. :Parameters: value : string the value of the property ref : string reference to an external resource, e.g. "NOAA:depth" applies_to : string 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'). datatype : string 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'). unit : string (optional) the unit of the property, e.g. "METRIC:m" id_ref : Id (optional) allows to attached a property specifically to one element (on the xml-level) r>noderZr! phylogeny annotation parent_branch> xsd:intxsd:bytexsd:datexsd:gDayxsd:longxsd:time xsd:float xsd:gYear xsd:short xsd:token xsd:anyURI xsd:double xsd:gMonth xsd:string xsd:boolean xsd:decimal xsd:integer xsd:dateTime xsd:duration xsd:gMonthDay xsd:hexBinaryxsd:gYearMonthxsd:unsignedIntxsd:base64Binaryxsd:unsignedBytexsd:unsignedLongxsd:unsignedShortxsd:negativeIntegerxsd:positiveIntegerxsd:normalizedStringxsd:nonNegativeIntegerxsd:nonPositiveIntegerNcCs`t||jjt||jjt||jjt||jj||_||_||_||_ ||_ ||_ dS)z)Initialize value for the Property object.N) rrr ok_applies_tor ok_datatyperid_refrAr applies_todatatype)r"rArr2r3rr1rrrr#s zProperty.__init__r<) r rrrrrrr/r0r#rrrrr s  #r c@s.eZdZdZd ddZeddZddZdS) ProteinDomainaRepresents 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: start : non-negative integer start of the domain on the sequence, using 0-based indexing end : non-negative integer end of the domain on the sequence confidence : float can be used to store e.g. E-values id : string unique identifier/name NcCr)z,Initialize value for a ProteinDomain object.N)rAstartendrrJ)r"rAr5r6rrJrrrr#rzProteinDomain.__init__cCs"t|j|jj|jj|jddS)z,Create ProteinDomain object from SeqFeature.r)r)r4rJlocationr5r6 qualifiersget)rUfeatrrrfrom_seqfeatures  zProteinDomain.from_seqfeaturecCsFtt|j|j|jd}z|j}Wn tyY|Sw||jd<|S)z2Create a SeqFeature from the ProteinDomain Object.)r7rJr)rrr5r6rArrr8)r"r:rrrr to_seqfeature s   zProteinDomain.to_seqfeaturer<)r rrrr#rr;r<rrrrr4s    r4c@s$eZdZdZedZdddZdS) ReferencezLiterature reference for a clade. NB: Whenever possible, use the ``doi`` attribute instead of the free-text ``desc`` element. z[a-zA-Z0-9_\.]+/[a-zA-Z0-9_\.]+NcCr)z2Initialize elements of the Reference class object.N)rre_doirdoir)r"r?rrrrr# rzReference.__init__r<)r rrrrrr>r#rrrrr=s r=c@sZeZdZdZhdZedZ            d ddZe d ddZ d d Z dS) raaA molecular sequence (Protein, DNA, RNA) associated with a node. One intended use for ``id_ref`` is to link a sequence to a taxonomy (via the taxonomy's ``id_source``) in case of multiple sequences and taxonomies per node. :Parameters: type : {'dna', 'rna', 'protein'} type of molecule this sequence represents id_ref : string reference to another resource id_source : string source for the reference symbol : string short symbol of the sequence, e.g. 'ACTM' (max. 10 chars) accession : Accession accession code for this sequence. name : string full name of the sequence, e.g. 'muscle Actin' location location of a sequence on a genome/chromosome. mol_seq : MolSeq the molecular sequence itself uri : Uri link annotations : list of Annotation objects annotations on this sequence domain_architecture : DomainArchitecture protein domains on this sequence other : list of Other objects non-phyloXML elements >dnarnaproteinz\S{1,10}Nc Cspt||jjt||jj||_||_||_||_||_ ||_ ||_ ||_ | |_ | |_| p/g|_| p4g|_dS)z'Initialize value for a Sequence object.N)rtypesr re_symbolrr)r1rsymbol accessionr*r7rbrdomain_architecture annotationsr!) r"r)r1rrErFr*r7rbrrGrHr!rrrr#Ms zSequence.__init__cCs|dur d|jv}t|jd|j|jtt|j|d}|jd}|dur@d|vr/d|d<nd |vr8d |d<nd |vr@d |d<d D]}||jvrP|j|||<qBt |jd t rft di|jd |d <|jdrg|d<|jdD]B}i}dD] }||vr||||<q{t |dt rt |d|d<t |dt rdd|dD|d<|dtdi|qu|jrtt|jdd|jDd|d<tdi|S)z7Create a new PhyloXML Sequence from a SeqRecord object.N-)rFrEr*rb molecule_typeDNAr@r)RNArArB)r1rr7rrH)rrrr)rrrPcSs$g|]}t|trtdi|qS)r)r$dictr rkproprrrrs  z+Sequence.from_seqrecord..cSsg|]}t|qSr)r4r;)rkr:rrrrs rrGr)rlrrJr*rKrr'rHr9r$rNUrilistrrrrfeaturesrr3ra)rUrwrcparamsrKrannotann_argsrrrfrom_seqrecordosX          zSequence.from_seqrecordc sddtt|jjfit|j|j|jd}|jr(dd|jj D|_ |j dkr0d}n|j dkr8d }n |j d kr@d }nd }|j |j |j|joY|jj|jj|jj d ||joffd d|jDd|_|S)aCreate 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], } cSsdd|DS)z+Remove None-valued items from a dictionary.cSsi|] \}}|dur||qSrir)rkrrrrr sz=Sequence.to_seqrecord..clean_dict..)r)dctrrr clean_dictrz)Sequence.to_seqrecord..clean_dict)rJr*rKcSsg|]}|qSr)r<)rkdomrrrrsz)Sequence.to_seqrecord..r@rLrArMrBNrArr)c sLg|]"}|j|j|j|j|jo|jj|jjgfdd|jDdqS)c s.g|]}|j|j|j|j|j|jdqS)rArr2r3rr1r]rOrZrrrs z4Sequence.to_seqrecord...)rrrr)rrP)rrrr)rrArP)rkannr^rrrs  )r1rr7rrKrH)r rrbrAr'rFrEr*rGrrSr)r1rr7rrrH)r"seqrecrKrr^rrjsR      +zSequence.to_seqrecord) NNNNNNNNNNNNri) r rrrrCrrrDr#rrWrjrrrrra's("  "  6rac@s"eZdZdZhdZdddZdS)SequenceRelationa1Express 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_0 : Id first sequence reference identifier id_ref_1 : Id second sequence reference identifier distance : float distance between the two sequences type : restricted string describe the type of relationship confidence : Confidence confidence value for this relation >r!rparalogyxenology orthologyultra_paralogysuper_orthologyone_to_one_orthologyNcCs0t||jj||_||_||_||_||_dSzInitialize the class.N)rrrrr)rrrrrrrr#.s  zSequenceRelation.__init__r<)r rrrrr#rrrrras rac@sHeZdZdZedZhdZ          d ddZddZ dS) ra:Describe taxonomic information for a clade. :Parameters: id_source : Id link other elements to a taxonomy (on the XML level) id : Id unique identifier of a taxon, e.g. Id('6500', provider='ncbi_taxonomy') for the California sea hare code : restricted string store UniProt/Swiss-Prot style organism codes, e.g. 'APLCA' for the California sea hare 'Aplysia californica' scientific_name : string the standard scientific name for this organism, e.g. 'Aplysia californica' for the California sea hare authority : string keep the authority, such as 'J. G. Cooper, 1863', associated with the 'scientific_name' common_names : list of strings common names for this organism synonyms : list of strings synonyms for this taxon? rank : restricted string taxonomic rank uri : Uri link other : list of Other objects non-phyloXML elements z[a-zA-Z0-9_]{2,10}>0formclassgenusorderr!tribebranchcohortdomainfamilylegionphylumkingdomspeciessubformrvarietycultivardivisionsubclasssubgenussubordersubtribe subcohort subfamily sublegion subphylum infraclass infratribe subkingdom subspecies subvariety superclass superorder supertribe infracohort infralegion infraphylum microphylum subdivision supercohort superfamily superlegion superphylum infrakingdom superspecies infradivision superdivisionNc Csht||jjt||jj||_||_||_||_||_ ||_ ||_ |p&g|_ | p+g|_ | p0g|_dSrh)rre_coderok_rankrrrJcodescientific_name authorityrankr common_namessynonymsr!) r"rrJrrrrrrrr!rrrr#s  zTaxonomy.__init__cCsL|jdur|jS|jdur|jS|jdur|jS|jdur"t|jS|jjS)rN)rrrrJr'r8r r0rrrr;s     zTaxonomy.__str__) NNNNNNNNNN) r rrrrrrrr#r;rrrrr8s  6 rc@r=)rQzA 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'). NcCs||_||_||_dSrhr\)r"rArr)rrrr#s z Uri.__init__cCs|jr|jSt|S)z$Return string representation of Uri.)rAreprr0rrrr;sz Uri.__str__r<rrrrrrQs  rQ)0rrrBior Bio.Alignrr Bio.PhylorBio.SeqrBio.SeqFeaturerr Bio.SeqRecordr r r TreeElementrrr>TreerDrQrrrrrrrrrrrrSrrr r r4r=rararrQrrrrsT          9"48 4!&PT2i)~