Class Hierarchy

• obitools.alignment.AlignedSequence
• obitools.svg.Circle
• obitools.gzip.GzipFile: The GzipFile class simulates most of the methods of a file object with the exception of the readinto() and truncate() methods.
• obitools.svg.Line
• obitools.svg.Rectangle
• obitools.SVGdraw.SVGelement: SVGelement(type,attributes,elements,text,namespace,**args) Creates a arbitrary svg element and is intended to be subclassed not used on its own.
  • obitools.SVGdraw.animate: an=animate(attribute,from,to,during,**args)
  • obitools.SVGdraw.animateColor: ac=animateColor(attribute,type,from,to,dur,**args)
  • obitools.SVGdraw.animateMotion: an=animateMotion(pathdata,dur,**args)
  • obitools.SVGdraw.animateTransform: antr=animateTransform(type,from,to,dur,**args)
  • obitools.SVGdraw.circle: c=circle(x,y,radius,fill,stroke,stroke_width,**args)
    • obitools.SVGdraw.point: p=point(x,y,color)
  • obitools.SVGdraw.cursor: c=cursor(url,**args)
  • obitools.SVGdraw.defs: d=defs(**args)
  • obitools.SVGdraw.description: d=description(text,**args)
  • obitools.SVGdraw.ellipse: e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
  • obitools.SVGdraw.group: g=group(id,**args)
  • obitools.SVGdraw.image: im=image(url,width,height,x,y,**args)
  • obitools.SVGdraw.line: l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
  • obitools.SVGdraw.lineargradient: lg=lineargradient(x1,y1,x2,y2,id,**args)
  • obitools.SVGdraw.link: a=link(url,**args)
  • obitools.SVGdraw.marker: m=marker(id,viewbox,refX,refY,markerWidth,markerHeight,**args)
  • obitools.SVGdraw.path: p=path(path,fill,stroke,stroke_width,**args)
  • obitools.SVGdraw.pattern: p=pattern(x,y,width,height,patternUnits,**args)
  • obitools.SVGdraw.polygon: pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
  • obitools.SVGdraw.polyline: pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
  • obitools.SVGdraw.radialgradient: rg=radialgradient(cx,cy,r,fx,fy,id,**args)
  • obitools.SVGdraw.rect: r=rect(width,height,x,y,fill,stroke,stroke_width,**args)
  • obitools.SVGdraw.script: sc=script(type,type,cdata,**args)
  • obitools.SVGdraw.set: st=set(attribute,to,during,**args)
  • obitools.SVGdraw.stop: st=stop(offset,stop_color,**args)
  • obitools.SVGdraw.style: st=style(type,cdata=None,**args)
  • obitools.SVGdraw.svg: s=svg(viewbox,width,height,**args)
  • obitools.SVGdraw.switch: sw=switch(**args)
  • obitools.SVGdraw.symbol: sy=symbol(id,viewbox,**args)
  • obitools.SVGdraw.text: t=text(x,y,text,font_size,font_family,**args)
  • obitools.SVGdraw.textpath: tp=textpath(text,link,**args)
  • obitools.SVGdraw.title: t=title(text,**args)
  • obitools.SVGdraw.tref: tr=tref(link='',**args)
  • obitools.SVGdraw.tspan: ts=tspan(text='',**args)
  • obitools.SVGdraw.use: u=use(link,x,y,width,height,**args)
  • obitools.SVGdraw.view: v=view(id,**args)
• obitools.svg.Scene
• obitools.svg.Text
• obitools.zipfile.ZipExtFile: File-like object for reading an archive member.
• obitools.zipfile.ZipFile: Class with methods to open, read, write, close, list zip files.
  • obitools.zipfile.PyZipFile: Class to create ZIP archives with Python library files and packages.
• obitools.zipfile._ZipDecrypter: Class to handle decryption of files stored within a ZIP archive.
• obitools.SVGdraw.drawing: d=drawing()
• object: The most base type
  • obitools.seqdb.AnnotatedSequence
    • obitools.seqdb.AnnotatedAASequence
      • obitools.seqdb.genbank.GpepSequence: Class used to represent a peptidic sequence issued from Genpep.
    • obitools.seqdb.AnnotatedNucSequence
      • obitools.seqdb.embl.EmblSequence: Class used to represent a nucleic sequence issued from EMBL.
      • obitools.seqdb.genbank.GbSequence: Class used to represent a nucleic sequence issued from Genbank.
  • exceptions.BaseException: Common base class for all exceptions
    • exceptions.Exception: Common base class for all non-exit exceptions.
      • obitools.zipfile.BadZipfile
      • obitools.obo.parser.FileFormatError: An error derived from the class Exception.
      • obitools.zipfile.LargeZipFile: Raised when writing a zipfile, the zipfile requires ZIP64 extensions and those extensions are disabled.
      • exceptions.StandardError: Base class for all standard Python exceptions that do not represent interpreter exiting.
        • exceptions.AssertionError: Assertion failed.
      • obitools.seqdb.dnaparser.UnknownFormatError
  • obitools.BioSequence: BioSequence class is the base class for biological sequence representation.
    • obitools.AASequence
      • obitools.seqdb.AnnotatedAASequence
        • obitools.seqdb.genbank.GpepSequence: Class used to represent a peptidic sequence issued from Genpep.
    • obitools.NucSequence
      • obitools.seqdb.AnnotatedNucSequence
        • obitools.seqdb.embl.EmblSequence: Class used to represent a nucleic sequence issued from EMBL.
        • obitools.seqdb.genbank.GbSequence: Class used to represent a nucleic sequence issued from Genbank.
      • obitools.solexa.SolexaSequence
      • obitools.tagmatcher.TagMatcherSequence: Class used to represent a nucleic sequence issued mapped on a genome by the tagMatcher software.
    • obitools.WrappedBioSequence
      • obitools.DNAComplementSequence
      • obitools.align.homopolymere.HomoNucBioSeq: classdocs
      • obitools.SubSequence
  • obitools.blast.Blast: Run blast
    • obitools.blast.NetBlast: Run blast on ncbi servers
  • obitools.utils.CachedDB
  • obitools.utils.ColumnFile
    • obitools.ecopcr.EcoPCRFile
    • obitools.ecotag.parser.EcoTagAbstractIterator
    • obitools.ecotag.parser.EcoTagFileIterator
    • obitools.goa.parser.GoAFileIterator
    • obitools.solexa.SolexaFile
  • obitools.obischemas.kb.Connection
  • obitools.obischemas.kb.Connection
  • obitools.obischemas.kb.Cursor
  • obitools.obischemas.kb.Cursor
  • obitools.distances.DistanceMatrix
    • obitools.distances.observed.Pairewise: Observed divergeance matrix from an alignment.
    • obitools.distances.observed.PairewiseGapRemoval: Observed divergeance matrix from an alignment.
  • obitools.eutils.EUtils
    • obitools.eutils.EFetch
      • obitools.seqdb.genbank.ncbi.NCBIAccession
      • obitools.seqdb.genbank.ncbi.NCBIGenbank
      • obitools.seqdb.genbank.ncbi.NCBIGenpep
  • obitools.ecopcr.annotation.EcoPCRDBAnnotationWriter: Class used to write Annotation description in EcoPCRDB format.
  • obitools.ecopcr.EcoPCRDBFile
    • obitools.ecopcr.sequence.EcoPCRDBSequenceIterator: Build an iterator over the sequences include in a sequence database formated for ecoPCR
    • obitools.ecopcr.taxonomy.EcoTaxonomyDB: A taxonomy database class
  • obitools.ecopcr.sequence.EcoPCRDBSequenceWriter
  • obitools.graph.Edge
    • obitools.phylogeny.PhylogenicEdge
  • obitools.format.ontology.go_obo.Entry: a Stanza entry, like [Typedef] for example
  • obitools.fast.Fast
  • obitools.carto.Feature
    • obitools.carto.MultiPartFeature
    • obitools.carto.SimpleFeature
      • obitools.carto.BoxFeature
    • obitools.carto.TagFeature
  • obitools.format.genericparser.GenericParser
  • obitools.graph.Graph: Class used to represent directed or undirected graph.
    • obitools.graph.DiGraph
      • obitools.graph.dag.DAG
        • obitools.graph.rootedtree.RootedTree
    • obitools.graph.UndirectedGraph
      • obitools.graph.tree.Forest
        • obitools.phylogeny.PhylogenicTree
  • obitools.format.ontology.go_obo.Header: class representing a GO header.
  • obitools.statistics.noncentralhypergeo.Interval
  • obitools.parallel.jobqueue.Job
  • obitools.parallel.jobqueue.JobIterator
  • obitools.carto.Level
  • obitools.location.Location: Define a location on a sequence.
    • obitools.location.ComplementLocation
    • obitools.location.CompositeLocation
    • obitools.location.feature.Feature
    • obitools.location.PointLocation: A point location describes a location on a sequence limited to a single position
    • obitools.location.SimpleLocation: A simple location is describe a continuous region of a sequence define by a begin and a end position.
  • obitools.carto.Map: Map represente une instance d'une carte genetique physique.
  • obitools.graph.Node
    • obitools.graph.dag.DAGNode
      • obitools.graph.rootedtree.RootedTreeNode
    • obitools.graph.tree.TreeNode
      • obitools.phylogeny.PhylogenicNode
  • obitools.format.ontology.go_obo.OBOFile: Iterator over all entries of an OBO file
  • obitools.statistics.noncentralhypergeo.Product
  • obitools.format.ontology.go_obo.RelatedTerm: RelatedTerm.relation RelatedTerm relation RelatedTerm.related_term RelatedTerm GO identifier RelatedTerm.comment all terms have 0 or 1 comment
  • obitools.sequenceencoder.SequenceEncoder
    • obitools.sequenceencoder.DNAComplementEncoder
    • obitools.sequenceencoder.SeqFragmentEncoder
  • obitools.align.ssearch.SsearchParser
  • obitools.carto.SubLevel
  • obitools.table.TableIteratorAsDict
  • obitools.table.TableRow
    • obitools.blast.BlastMatch: Blast high scoring pair between two sequences
  • obitools.tagmatcher.parser.TagMatcherIterator
  • obitools.obo.parser.TaggedValue: A couple 'tag:value' of an OBOEntry.
    • obitools.obo.parser.DefValue: A couple 'def:value' inherited from the class TaggedValue.
    • obitools.obo.parser.NameValue: A couple 'name:value' inherited from the class TaggedValue.
    • obitools.obo.parser.NamespaceValue
    • obitools.obo.parser.RelationshipValue: A couple 'xref:value' inherited from the class TaggedValue.
    • obitools.obo.parser.RemarkValue
    • obitools.obo.parser.SynonymValue: A couple 'synonym:value' inherited from the class TaggedValue.
    • obitools.obo.parser.XrefValue: A couple 'xref:value' inherited from the class TaggedValue.
  • obitools.parallel.Task
  • obitools.parallel.TaskPool
  • obitools.ecopcr.taxonomy.Taxonomy
    • obitools.ecopcr.taxonomy.EcoTaxonomyDB: A taxonomy database class
    • obitools.ecopcr.taxonomy.TaxonomyDump
  • obitools.format.ontology.go_obo.Term: representing a GO term.
  • unittest.TestCase: A class whose instances are single test cases.
    • obitools.unit.obitools.BioseqTest
      • obitools.unit.obitools.AABioseqTest: Test obitools.AASequence class
      • obitools.unit.obitools.NucBioseqTest: Test obitools.NucSequence class
  • obitools.tree.TreeNode
  • obitools.WrapperSetIterator
  • obitools.obo.parser.Xref: A xref object of an OBOentry.
  • obitools.format.ontology.go_obo.Xref: Xref.db Xref database Xref.id Xref identifier
  • obitools.zipfile.ZipInfo: Class with attributes describing each file in the ZIP archive.
  • dict: dict() -> new empty dictionary.
    • obitools.ecotag.EcoTagResult
    • obitools.location.feature.Feature
    • obitools.graph.Indexer: Allow to manage convertion between an arbitrarly hashable python value and an unique integer key
    • obitools.parallel.jobqueue.JobPool: JobPool is dedicated to manage a job queue.
    • obitools.tree.layout.NodeLayout: Layout data associated to a tree node.
    • obitools.obo.parser.OBOEntry: An entry of an OBOFile.
      • obitools.obo.go.parser.GOEntry: An entry of a GeneOntology .obo file.
      • obitools.obo.parser.OBOTerm: A stanza named 'Term'.
        • obitools.obo.go.parser.GOTerm: A stanza named 'Term'.
    • obitools.obo.parser.TrailingModifier: A class object which inherits from the class dict.
    • obitools.tree.layout.TreeLayout: Description of a phylogenetic tree layout
  • obitools.table.iTableIterator
    • obitools.blast.BlastResultIterator
    • obitools.table.ProjectionIterator
    • obitools.table.SelectionIterator
      • obitools.blast.BlastCovMinFilter
    • obitools.table.TableIterator
    • obitools.table.UnionIterator
  • list: list() -> new list list(sequence) -> new list initialized from sequence's items
    • obitools.alignment.Alignement
    • obitools.align.Alignement
    • obitools.cns.quality.QualitySequence
    • obitools.table.Table: Tables are list of rows of the same model
      • obitools.blast.BlastResult: Results of a blast run
    • obitools.table._Row
  • set: set(iterable) --> set object
    • obitools.tree.Tree
    • obitools.WrapperSet
• obitools.SVGdraw.pathdata: class used to create a pathdata object which can be used for a path.
• obitools.SVGdraw.spannedtext: st=spannedtext(textlist=[])