Package Bio

Collection of modules for dealing with biological data in Python.

The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.

http://biopython.org

Version: 1.56

Submodules

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Bio.Affy: Deal with Affymetrix related data such as cel files.
- Bio.Affy.CelFile: Classes for accessing the information in Affymetrix cel files.
Bio.Align: Code for dealing with sequence alignments.
- Bio.Align.AlignInfo: Extract information from alignment objects.
- Bio.Align.Applications: Alignment command line tool wrappers.
  - Bio.Align.Applications._Clustalw: Command line wrapper for the multiple alignment program Clustal W.
  - Bio.Align.Applications._Dialign: Bio.Application command line for the multiple alignment program DIALIGN2-2.
  - Bio.Align.Applications._Mafft: Command line wrapper for the multiple alignment programme MAFFT.
  - Bio.Align.Applications._Muscle: Command line wrapper for the multiple alignment program MUSCLE.
  - Bio.Align.Applications._Prank: Command line wrapper for the multiple alignment program PRANK.
  - Bio.Align.Applications._Probcons: Command line wrapper for the multiple alignment program PROBCONS.
  - Bio.Align.Applications._TCoffee: Command line wrapper for the multiple alignment program TCOFFEE.
- Bio.Align.Generic: Contains classes to deal with generic sequence alignment stuff not specific to a particular program or format.
Bio.AlignIO: Multiple sequence alignment input/output as alignment objects.
- Bio.AlignIO.ClustalIO: Bio.AlignIO support for the "clustal" output from CLUSTAL W and other tools.
- Bio.AlignIO.EmbossIO: Bio.AlignIO support for the "emboss" alignment output from EMBOSS tools.
- Bio.AlignIO.FastaIO: Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools.
- Bio.AlignIO.Interfaces: AlignIO support module (not for general use).
- Bio.AlignIO.NexusIO: Bio.AlignIO support for the "nexus" file format.
- Bio.AlignIO.PhylipIO: AlignIO support for the "phylip" format used in Joe Felsenstein's PHYLIP tools.
- Bio.AlignIO.StockholmIO: Bio.AlignIO support for the "stockholm" format (used in the PFAM database).
Bio.Alphabet: Alphabets used in Seq objects etc to declare sequence type and letters.
- Bio.Alphabet.IUPAC: Standard nucleotide and protein alphabets defined by IUPAC.
- Bio.Alphabet.Reduced: Reduced alphabets which lump together several amino-acids into one letter.
Bio.Application: General mechanisms to access applications in Biopython.
Bio.Blast: Code for dealing with BLAST programs and output.
- Bio.Blast.Applications: Definitions for interacting with BLAST related applications.
- Bio.Blast.NCBIStandalone: Code for calling standalone BLAST and parsing plain text output (OBSOLETE).
- Bio.Blast.NCBIWWW: This module provides code to work with the WWW version of BLAST provided by the NCBI.
- Bio.Blast.NCBIXML: This module provides code to work with the BLAST XML output following the DTD available on the NCBI FTP ftp://ftp.ncbi.nlm.nih.gov/blast/documents/xml/NCBI_BlastOutput.dtd
- Bio.Blast.ParseBlastTable: A parser for the NCBI blastpgp version 2.2.5 output format.
- Bio.Blast.Record: Record classes to hold BLAST output.
Bio.CAPS: This module deals with CAPS markers.
Bio.Clustalw: Code for calling ClustalW and parsing its output (DEPRECATED).
Bio.Cluster
Bio.Compass: Code to deal with COMPASS output, a program for profile/profile comparison.
Bio.Crystal: Module to represent the NDB Atlas structure (a minimal subset of PDB format).
Bio.Data: Collections of various bits of useful biological data.
- Bio.Data.CodonTable: Codon tables based on those from the NCBI.
- Bio.Data.IUPACData
Bio.DocSQL: Bio.DocSQL: easy access to DB API databases.
Bio.Emboss: Code to interact with the ever-so-useful EMBOSS programs.
- Bio.Emboss.Applications: Code to interact with and run various EMBOSS programs.
- Bio.Emboss.Primer3: Code to parse output from the EMBOSS eprimer3 program.
- Bio.Emboss.PrimerSearch: Code to interact with the primersearch program from EMBOSS.
Bio.Encodings: Properties once used for transcription and translation (DEPRECATED).
- Bio.Encodings.IUPACEncoding: Properties once used for transcription and translation (DEPRECATED).
Bio.Entrez: Provides code to access NCBI over the WWW.
- Bio.Entrez.Parser: Parser for XML results returned by NCBI's Entrez Utilities.
Bio.Enzyme: Module to work with enzyme.dat file (DEPRECATED).
Bio.ExPASy: This module provides code to access resources at ExPASy over the WWW.
- Bio.ExPASy.Enzyme: This module provides code to work with the enzyme.dat file from Enzyme.
- Bio.ExPASy.Prodoc: This module provides code to work with the prosite.doc file from Prosite.
- Bio.ExPASy.Prosite: This module provides code to work with the prosite dat file from Prosite.
- Bio.ExPASy.ScanProsite
Bio.FSSP: Parser for FSSP files, used in a database of protein fold classifications.
- Bio.FSSP.FSSPTools
- Bio.FSSP.fssp_rec
Bio.File: Code for more fancy file handles.
Bio.GA: A selection of genetic algorithm code.
- Bio.GA.Crossover
  - Bio.GA.Crossover.General: General functionality for crossover that doesn't apply.
  - Bio.GA.Crossover.GeneralPoint: Generalized N-Point Crossover.
  - Bio.GA.Crossover.Point: Perform two-point crossovers between the genomes of two organisms.
  - Bio.GA.Crossover.TwoPoint: Perform two-point crossovers between the genomes of two organisms.
  - Bio.GA.Crossover.Uniform: Perform uniform crossovers between the genomes of two organisms.
- Bio.GA.Evolver: Evolution Strategies for a Population.
- Bio.GA.Mutation
  - Bio.GA.Mutation.General: General functionality for mutations.
  - Bio.GA.Mutation.Simple: Perform Simple mutations on an organism's genome.
- Bio.GA.Organism: Deal with an Organism in a Genetic Algorithm population.
- Bio.GA.Repair
  - Bio.GA.Repair.Stabilizing: Methods for performing repairs that will Stabilize genomes.
- Bio.GA.Selection
  - Bio.GA.Selection.Abstract: Base selection class from which all Selectors should derive.
  - Bio.GA.Selection.Diversity: Select individuals into a new population trying to maintain diversity.
  - Bio.GA.Selection.RouletteWheel: Implement Roulette Wheel selection on a population.
  - Bio.GA.Selection.Tournament: Provide Tournament style selection.
Bio.GFF: Access to General Feature Format databases created with BioPerl (DEPRECATED).
- Bio.GFF.GenericTools: A set of generic bits of code under Bio.GFF (DEPRECATED).
- Bio.GFF.binning: Binning support for Bio.GFF (DEPRECATED)
- Bio.GFF.easy: Bio.GFF.easy: some functions to ease the use of Biopython (DEPRECATED)
Bio.GenBank: Code to work with GenBank formatted files.
- Bio.GenBank.LocationParser: Code used for parsing GenBank/EMBL feature location strings (DEPRECATED).
- Bio.GenBank.Record: Hold GenBank data in a straightforward format.
- Bio.GenBank.Scanner
- Bio.GenBank.utils: Useful utilities for helping in parsing GenBank files.
Bio.Geo: Parser for files from NCBI's Gene Expression Omnibus (GEO).
- Bio.Geo.Record: Hold GEO data in a straightforward format.
Bio.Graphics: Bio.Graphics offsers several graphical ouputs, all using ReportLab.
- Bio.Graphics.BasicChromosome: Draw representations of organism chromosomes with added information.
- Bio.Graphics.Comparative: Plots to compare information between different sources.
- Bio.Graphics.DisplayRepresentation: Represent information for graphical display.
- Bio.Graphics.Distribution: Display information distributed across a Chromosome-like object.
- Bio.Graphics.GenomeDiagram
  - Bio.Graphics.GenomeDiagram._AbstractDrawer: AbstractDrawer module (considered to be a private module, the API may change!)
  - Bio.Graphics.GenomeDiagram._CircularDrawer: CircularDrawer module
  - Bio.Graphics.GenomeDiagram._Colors: Colors module
  - Bio.Graphics.GenomeDiagram._Diagram: Diagram module
  - Bio.Graphics.GenomeDiagram._Feature: Feature module
  - Bio.Graphics.GenomeDiagram._FeatureSet: FeatureSet module
  - Bio.Graphics.GenomeDiagram._Graph: Graph module
  - Bio.Graphics.GenomeDiagram._GraphSet: GraphSet module
  - Bio.Graphics.GenomeDiagram._LinearDrawer: LinearDrawer module
  - Bio.Graphics.GenomeDiagram._Track: Track module
Bio.HMM: A selection of Hidden Markov Model code.
- Bio.HMM.DynamicProgramming: Dynamic Programming algorithms for general usage.
- Bio.HMM.MarkovModel: Deal with representations of Markov Models.
- Bio.HMM.Trainer: Provide trainers which estimate parameters based on training sequences.
- Bio.HMM.Utilities: Generic functions which are useful for working with HMMs.
Bio.HotRand: handles true random numbers supplied from the the web server of fourmilab.
Bio.Index: Index.py
Bio.InterPro: This module provides code to work with html files from InterPro, and code to access resources at InterPro over the WWW.
Bio.KDTree: The KD tree data structure can be used for all kinds of searches that involve N-dimensional vectors.
- Bio.KDTree.KDTree: KD tree data structure for searching N-dimensional vectors.
Bio.KEGG: This module provides code to work with data from the KEGG database.
- Bio.KEGG.Compound: This module provides code to work with the KEGG Ligand/Compound database.
- Bio.KEGG.Enzyme: This module provides code to work with the KEGG Enzyme database.
- Bio.KEGG.Map: This module provides code to import KEGG Pathway maps for use with the Biopython Pathway module.
Bio.LogisticRegression: This module provides code for doing logistic regressions.
Bio.MarkovModel: This is an implementation of a state-emitting MarkovModel.
Bio.MaxEntropy: Maximum Entropy code.
Bio.Medline: This module provides code to work with Medline.
Bio.Motif: Module containing different tools for sequence motif analysis.
- Bio.Motif.Applications: Motif command line tool wrappers.
  - Bio.Motif.Applications._AlignAce: This module provides code to work with the standalone version of AlignACE, for motif search in DNA sequences.
- Bio.Motif.Parsers
  - Bio.Motif.Parsers.AlignAce: Parsing AlignACE and CompareACE files: AlignAceParser,CompareAceParser
  - Bio.Motif.Parsers.MAST
  - Bio.Motif.Parsers.MEME
- Bio.Motif.Thresholds: Approximate calculation of appropriate thresholds for motif finding
- Bio.Motif._Motif: Implementation of sequence motifs (PRIVATE).
Bio.NMR: Code for working with NMR data
- Bio.NMR.NOEtools
- Bio.NMR.xpktools
Bio.NaiveBayes: This provides code for a general Naive Bayes learner.
Bio.NeuralNetwork
- Bio.NeuralNetwork.BackPropagation
  - Bio.NeuralNetwork.BackPropagation.Layer: Model a single layer in a nueral network.
  - Bio.NeuralNetwork.BackPropagation.Network: Represent Neural Networks.
- Bio.NeuralNetwork.Gene
  - Bio.NeuralNetwork.Gene.Motif: Find and deal with motifs in biological sequence data.
  - Bio.NeuralNetwork.Gene.Pattern: Generic functionality useful for all gene representations.
  - Bio.NeuralNetwork.Gene.Schema: Deal with Motifs or Signatures allowing ambiguity in the sequences.
  - Bio.NeuralNetwork.Gene.Signature: Find and deal with signatures in biological sequence data.
- Bio.NeuralNetwork.StopTraining: Classes to help deal with stopping training a neural network.
- Bio.NeuralNetwork.Training: Provide classes for dealing with Training Neural Networks.
Bio.Nexus: The Bio.Nexus contains a NEXUS file parser and objects to model this data.
- Bio.Nexus.Nexus: Nexus class.
- Bio.Nexus.Nodes
- Bio.Nexus.Trees: Tree class to handle phylogenetic trees.
Bio.PDB: Classes that deal with macromolecular crystal structures.
- Bio.PDB.AbstractPropertyMap: Class that maps (chain_id, residue_id) to a residue property.
- Bio.PDB.Atom: Atom class, used in Structure objects.
- Bio.PDB.Chain: Chain class, used in Structure objects.
- Bio.PDB.DSSP
- Bio.PDB.DSSP': Use the DSSP program to calculate secondary structure and accessibility.
- Bio.PDB.Dice
- Bio.PDB.Entity
- Bio.PDB.FragmentMapper
- Bio.PDB.FragmentMapper': Classify protein backbone structure according to Kolodny et al's fragment libraries.
- Bio.PDB.HSExposure: Half-sphere exposure and coordination number calculation.
- Bio.PDB.MMCIF2Dict: Turn an mmCIF file into a dictionary.
- Bio.PDB.MMCIFParser: mmCIF parser (partly implemented in C).
- Bio.PDB.Model: Model class, used in Structure objects.
- Bio.PDB.NACCESS
- Bio.PDB.NeighborSearch: Fast atom neighbor lookup using a KD tree (implemented in C++).
- Bio.PDB.PDBExceptions: Some Bio.PDB-specific exceptions.
- Bio.PDB.PDBIO
- Bio.PDB.PDBIO': Output of PDB files.
- Bio.PDB.PDBList
- Bio.PDB.PDBList': Access the PDB over the internet (for example to download structures).
- Bio.PDB.PDBParser
- Bio.PDB.PDBParser': Parser for PDB files.
- Bio.PDB.PSEA: Wrappers for PSEA, a program for secondary structure assignment.
- Bio.PDB.Polypeptide: Polypeptide-related classes (construction and representation).
- Bio.PDB.Residue
- Bio.PDB.ResidueDepth
- Bio.PDB.ResidueDepth': Calculation of residue depth using command line tool MSMS.
- Bio.PDB.Selection: Selection of atoms, residues, etc.
- Bio.PDB.Structure: The structure class, representing a macromolecular structure.
- Bio.PDB.StructureAlignment
- Bio.PDB.StructureAlignment': Map the residues of two structures to each other based on a FASTA alignment file.
- Bio.PDB.StructureBuilder: Consumer class that builds a Structure object.
- Bio.PDB.Superimposer
- Bio.PDB.Superimposer': Superimpose two structures.
- Bio.PDB.Vector
- Bio.PDB.Vector': Vector class, including rotation-related functions.
- Bio.PDB.mmCIF
- Bio.PDB.parse_pdb_header
- Bio.PDB.parse_pdb_header': Parse the header of a PDB file.
Bio.ParserSupport: Code to support writing parsers.
Bio.Parsers: Third party and other parsers useful internally to Biopython (DEPRECATED).
- Bio.Parsers.spark: Copy of John Aycock's SPARK parser included with Biopython (DEPRECATED).
Bio.Pathway: BioPython Pathway module.
- Bio.Pathway.Rep: BioPython Pathway support module.
  - Bio.Pathway.Rep.Graph
  - Bio.Pathway.Rep.HashSet
  - Bio.Pathway.Rep.MultiGraph
Bio.Phylo: Package for working with phylogenetic trees.
- Bio.Phylo.BaseTree: Base classes for Bio.Phylo objects.
- Bio.Phylo.Newick: Classes corresponding to Newick trees, also used for Nexus trees.
- Bio.Phylo.NewickIO: I/O function wrappers for the Newick file format.
- Bio.Phylo.NexusIO: I/O function wrappers for Bio.Nexus trees.
- Bio.Phylo.PhyloXML: Classes corresponding to phyloXML elements.
- Bio.Phylo.PhyloXMLIO: PhyloXML reader/parser, writer, and associated functions.
- Bio.Phylo._io: I/O function wrappers for phylogenetic tree formats.
- Bio.Phylo._sugar: Short helper functions (syntax sugar) used in Bio.Phylo.
- Bio.Phylo._utils: Utilities for handling, displaying and exporting Phylo trees.
Bio.PopGen: PopGen: Population Genetics and Genomics library in Python
- Bio.PopGen.Async: Support for asynchronous execution.
  - Bio.PopGen.Async.Local: Asynchronous local execution.
- Bio.PopGen.FDist: This module provides code to work with FDist.
  - Bio.PopGen.FDist.Async: This modules allows for asynchronous execution of Fdist and spliting of loads.
  - Bio.PopGen.FDist.Controller: This module allows to control fdist.
  - Bio.PopGen.FDist.Utils
- Bio.PopGen.GenePop: This module provides code to work with GenePop.
  - Bio.PopGen.GenePop.Controller: This module allows to control GenePop.
  - Bio.PopGen.GenePop.EasyController: This module allows to control GenePop through an easier interface.
  - Bio.PopGen.GenePop.FileParser: This class provides code to parse BIG GenePop files.
  - Bio.PopGen.GenePop.LargeFileParser: Large file parsing of Genepop files
  - Bio.PopGen.GenePop.Utils
- Bio.PopGen.SimCoal: SimCoal2 execution module and support functions.
  - Bio.PopGen.SimCoal.Async: This module allows to cache Simcoal2 results, and return on the fly in case the calculation was done.
  - Bio.PopGen.SimCoal.Cache: This module allows to cache Simcoal2 results, and return on the fly in case the calculation was done.
  - Bio.PopGen.SimCoal.Controller: This module allows you to control Simcoal2.
  - Bio.PopGen.SimCoal.Template
Bio.PropertyManager: Stores properties associated with the class of an object (DEPRECATED).
Bio.Prosite: Module for working with Prosite files from ExPASy (DEPRECATED).
- Bio.Prosite.Pattern
- Bio.Prosite.Prodoc: This module is OBSOLETE.
Bio.Restriction: Usage: =====
- Bio.Restriction.DNAUtils: DNA utilities for Bio.Restriction (DEPRECATED).
- Bio.Restriction.PrintFormat
- Bio.Restriction.RanaConfig
- Bio.Restriction.Restriction: Notes about the diverses class of the restriction enzyme implementation.
- Bio.Restriction.Restriction_Dictionary
- Bio.Restriction._Update
  - Bio.Restriction._Update.RestrictionCompiler: Convert a serie of Rebase files into a Restriction_Dictionary.py module.
  - Bio.Restriction._Update.Update: Update the Rebase emboss files used by Restriction to build the Restriction_Dictionary.py module.
Bio.SCOP: SCOP: Structural Classification of Proteins.
- Bio.SCOP.Cla: Handle the SCOP CLAssification file, which describes SCOP domains.
- Bio.SCOP.Des: Handle the SCOP DEScription file.
- Bio.SCOP.Dom: Handle the SCOP DOMain file.
- Bio.SCOP.Hie: Handle the SCOP HIErarchy files, which describe the SCOP hierarchy in terms of SCOP unique identifiers (sunid).
- Bio.SCOP.Raf: ASTRAL RAF (Rapid Access Format) Sequence Maps.
- Bio.SCOP.Residues
- Bio.SCOP.Residues'
Bio.SVDSuperimposer: SVDSuperimposer finds the best rotation and translation to put two point sets on top of each other (minimizing the RMSD).
- Bio.SVDSuperimposer.SVDSuperimposer
- Bio.SVDSuperimposer.SVDSuperimposer'
Bio.Search
Bio.Seq: Provides objects to represent biological sequences with alphabets.
Bio.SeqFeature: Represent a Sequence Feature holding info about a part of a sequence.
Bio.SeqIO: Sequence input/output as SeqRecord objects.
- Bio.SeqIO.AceIO: Bio.SeqIO support for the "ace" file format.
- Bio.SeqIO.FastaIO: Bio.SeqIO support for the "fasta" (aka FastA or Pearson) file format.
- Bio.SeqIO.IgIO: Bio.SeqIO support for the "ig" (IntelliGenetics or MASE) file format.
- Bio.SeqIO.InsdcIO: Bio.SeqIO support for the "genbank" and "embl" file formats.
- Bio.SeqIO.Interfaces: Bio.SeqIO support module (not for general use).
- Bio.SeqIO.PhdIO: Bio.SeqIO support for the "phd" file format.
- Bio.SeqIO.PirIO: Bio.SeqIO support for the "pir" (aka PIR or NBRF) file format.
- Bio.SeqIO.QualityIO: Bio.SeqIO support for the FASTQ and QUAL file formats.
- Bio.SeqIO.SffIO: Bio.SeqIO support for the binary Standard Flowgram Format (SFF) file format.
- Bio.SeqIO.SwissIO: Bio.SeqIO support for the "swiss" (aka SwissProt/UniProt) file format.
- Bio.SeqIO.TabIO: Bio.SeqIO support for the "tab" (simple tab separated) file format.
- Bio.SeqIO.UniprotIO: Bio.SeqIO support for the "uniprot-xml" file format.
- Bio.SeqIO._convert: Optimised sequence conversion code (PRIVATE).
- Bio.SeqIO._index: Dictionary like indexing of sequence files (PRIVATE).
Bio.SeqRecord: Represent a Sequence Record, a sequence with annotation.
Bio.SeqUtils: Miscellaneous functions for dealing with sequences.
- Bio.SeqUtils.CheckSum: Functions to calculate assorted sequence checksums.
- Bio.SeqUtils.CodonUsage
- Bio.SeqUtils.CodonUsageIndices
- Bio.SeqUtils.IsoelectricPoint: Calculate isoelectric points of polypeptides using methods of Bjellqvist.
- Bio.SeqUtils.MeltingTemp: Calculate the thermodynamic melting temperatures of nucleotide sequences.
- Bio.SeqUtils.ProtParam: Simple protein analysis.
- Bio.SeqUtils.ProtParamData
- Bio.SeqUtils.lcc
Bio.Sequencing: Code to deal with various programs for sequencing and assembly.
- Bio.Sequencing.Ace: Parser for ACE files output by PHRAP.
- Bio.Sequencing.Applications: Main entry point for application command line wrappers related to sequencing.
  - Bio.Sequencing.Applications._Novoalign: Command line wrapper for the short read aligner Novoalign by Novocraft (www.novocraft.com)
- Bio.Sequencing.Phd: Parser for PHD files output by PHRED and used by PHRAP and CONSED.
Bio.Statistics
- Bio.Statistics.lowess: This module implements the Lowess function for nonparametric regression.
Bio.SubsMat: Substitution matrices, log odds matrices, and operations on them.
- Bio.SubsMat.FreqTable
- Bio.SubsMat.MatrixInfo: A whole bunch of substitution matrices for use in alignments, etc.
Bio.SwissProt: This module provides code to work with the sprotXX.dat file from SwissProt.
- Bio.SwissProt.KeyWList: Code to parse the keywlist.txt file from SwissProt/UniProt
Bio.Transcribe: Code to transcribe DNA into RNA or back (DEPRECATED).
Bio.Translate: Code to translate DNA or RNA into proteins (DEPRECATED).
Bio.UniGene: Parse Unigene flat file format files such as the Hs.data file.
- Bio.UniGene.UniGene
Bio.Wise
- Bio.Wise.dnal
- Bio.Wise.psw
Bio._py3k: Python 3 compatibility tools (PRIVATE).
Bio.kNN: This module provides code for doing k-nearest-neighbors classification.
Bio.listfns: This provides useful general functions for working with lists (DEPRECATED).
Bio.pairwise2: This package implements pairwise sequence alignment using a dynamic programming algorithm.
Bio.triefind: Given a trie, find all occurrences of a word in the trie in a string.
Bio.utils: Miscellaneous functions for dealing with sequences (DEPRECATED).

Classes

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BiopythonDeprecationWarning
Biopython deprecation warning.

MissingExternalDependencyError
Missing an external dependency.

MissingPythonDependencyError
Missing an external python dependency (subclass of ImportError).

Variables

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__package__ = None
hash(x)