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Package Bio
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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
Submodules
  • Affy: Deal with Affymetrix related data such as cel files.
  • Ais: Immune system simulation based on ideas from Immunocomputing: a survey.
  • Align: Code for dealing with sequence alignments.
    • AlignInfo: Extract information from alignment objects.
    • FormatConvert: Utility for conversion between different formats for representing alignments.
    • Generic: Contains classes to deal with generic sequence alignment stuff not specific to a particular program or format.
  • AlignAce: Parser and code for dealing with the standalone version of AlignAce, a motif search program.
    • AlignAceStandalone: This module provides code to work with the standalone version of AlignACE, for motif search in DNA sequences.
    • Applications: Definitions for interacting with AlignAce.
    • CompareAceStandalone: This module provides code to work with the standalone version of CompareAce, for motif comparison
    • Motif: Implementation of sequence motifs.
    • Parser: Classes for pparsing AlignAce and CompareACE files
    • Scanner: Consumers for AlignACE and CompareACE parsers.
  • Alphabet
  • Application: General mechanisms to access applications in biopython.
  • Blast: Code for dealing with BLAST programs and output.
    • Applications: Definitions for interacting with Blast related applications.
    • NCBIStandalone: This module provides code to work with the standalone version of BLAST, either blastall or blastpgp, provided by the NCBI.
    • NCBIWWW: This module provides code to work with the WWW version of BLAST provided by the NCBI.
    • 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
    • ParseBlastTable
    • Record: Record classes to hold BLAST output.
  • builders
  • CAPS: This module deals with CAPS markers.
  • Compass: Code to deal with COMPASS output, a program for profile/profile comparison.
  • config
    • DBRegistry: Implements Registry to access databases.
    • FormatRegistry: Implements a Registry to store Martel-type format expressions.
    • Registry: This module implements some base classes used in the Registry system for Biopython.
    • SeqDBRegistry: This module handles seqdatabase.INI file.
    • _stanzaformat: This module reads and writes (actually, write not implemented yet) files in the OBF stanza format.
    • _support: Support code for dealing with registries.
  • crc
  • Crystal: Hetero, Crystal and Chain exist to represent the NDB Atlas structure.
  • Data: Collections of various bits of useful biological data.
  • dbdefs
  • DBXRef
  • Decode
  • distance: This module provides code for various distance measures.
  • Emboss: Code to interact with the ever-so-useful EMBOSS programs.
    • Applications: Code to interact with and run various EMBOSS programs.
    • Primer: Code to interact with various Primer-related programs from EMBOSS.
    • primer3_format: Martel definitions for the output files produced by primer3.
    • primersearch_format: Martel format for primersearch output files,
  • Encodings: Properties for functionality such as transcription and translation.
  • Enzyme: This module provides code to work with the enzyme.dat file from Enzyme.
  • EUtils: EUtils is a client-side library for the Entrez databases at NCBI.
    • Config: Configuration information about NCBI's databases
    • Datatypes: various EUtils datatypes
    • DBIdsClient: Search and retrieve information given a set of database identifiers.
    • dtd2py: Internal class to convert DTDs to python form.
    • DTDs
    • HistoryClient: Search and retreive information using the EUtils history.
    • Mixins: implements functionality shared between HistoryClient and DBIdsClient
    • MultiDict: Dictionary-like objects which allow multiple keys Python dictionaries map a key to a value.
    • parse
    • POM: This module implements the XML POM -- the Python Object Model for XML.
    • ReseekFile: Wrap a file handle to allow seeks back to the beginning Sometimes data coming from a socket or other input file handle isn't what it was supposed to be.
    • setup
    • sourcegen: This module can be used to generate python source code.
    • ThinClient: Low-level interface to NCBI's EUtils for Entrez search and retrieval.
  • expressions
    • blast
    • blocks
    • embl
      • embl65: Format from EMBL Nucleotide Sequence Database Release 65, December 2000
    • fasta
    • genbank: Martel based parser to read GenBank formatted files.
    • hmmpfam: Martel expression for the hmmpfam database search program in hmmer.
    • transfac: A Martel format to parse the output from transfac.
  • EZRetrieve: This module contains code to access EZRetrieve.
  • File: Code for more fancy file handles.
  • FilteredReader: Code for more fancy file handles.
  • formatdefs
  • FormatIO
  • FSSP
  • GA
    • Crossover
      • General: General functionality for crossover that doesn't apply.
      • GeneralPoint: Generalized N-Point Crossover.
      • Point: Perform two-point crossovers between the genomes of two organisms.
      • TwoPoint: Perform two-point crossovers between the genomes of two organisms.
      • Uniform: Perform uniform crossovers between the genomes of two organisms.
    • Evolver: Evolution Strategies for a Population.
    • Mutation
      • General: General functionality for mutations.
      • Simple: Perform Simple mutations on an organism's genome.
    • Organism: Deal with an Organism in a Genetic Algorithm population.
    • Repair
      • Stabilizing: Methods for performing repairs that will Stabilize genomes.
    • Selection
      • Abstract: Base selection class from which all Selectors should derive.
      • Diversity: Select individuals into a new population trying to maintain diversity.
      • RouletteWheel: Implement Roulette Wheel selection on a population.
      • Tournament: Provide Tournament style selection.
  • Gobase: This module provides code to work with files from Gobase.
  • Graphics
    • BasicChromosome: Draw representations of organism chromosomes with added information.
    • Comparative: Plots to compare information between different sources.
    • DisplayRepresentation: Represent information for graphical display.
    • Distribution: Display information distributed across a Chromosome-like object.
  • HMM
    • DynamicProgramming: Dynamic Programming algorithms for general usage.
    • MarkovModel: Deal with representations of Markov Models.
    • Trainer: Provide trainers which estimate parameters based on training sequences.
    • Utilities: Generic functions which are useful for working with HMMs.
  • HotRand: handles true random numbers supplied from the the web server of fourmilab.
  • Index: Index.py
  • InterPro: This module provides code to work with html files from InterPro.
  • KEGG: This module provides code to work with data from the KEGG database.
  • kNN: This module provides code for doing k-nearest-neighbors classification.
  • lcc
  • listfns: This provides useful general functions for working with lists.
  • LogisticRegression: This module provides code for doing logistic regressions.
  • MarkovModel: This is an implementation of a state-emitting MarkovModel.
  • MarkupEditor: Simplify adding markup to a piece of text.
  • mathfns: This provides useful general math tools.
  • MaxEntropy: Maximum Entropy code.
  • Medline: This module provides code to work with Medline.
  • MEME: Parser for dealing with text output from the MEME motif search program
  • Mindy
  • MultiProc: Code to schedule and run multiple processes.
    • copen: This implements a set of classes that wraps a file object interface around code that executes in another process.
    • Scheduler: Simple scheduling of threads to be run.
    • Task: Task.py
  • NaiveBayes: This provides code for a general Naive Bayes learner.
  • Ndb: This module provides code to work with html files from NDB.
  • NetCatch: NetCatch enables the user to scan a list of labelled urls and select a subset to read into a file.
  • NeuralNetwork
    • BackPropagation
      • Layer: Model a single layer in a nueral network.
      • Network: Represent Neural Networks.
    • Gene
      • Motif: Find and deal with motifs in biological sequence data.
      • Pattern: Generic functionality useful for all gene representations.
      • Schema: Deal with Motifs or Signatures allowing ambiguity in the sequences.
      • Signature: Find and deal with signatures in biological sequence data.
    • StopTraining: Classes to help deal with stopping training a neural network.
    • Training: Provide classes for dealing with Training Neural Networks.
  • Nexus
  • NMR: Code for working with NMR data
  • pairwise2: This package implements pairwise sequence alignment using a dynamic programming algorithm.
  • Parsers: Third party and other parsers useful internally to Biopython.
  • ParserSupport: Code to support writing parsers.
  • Pathway: BioPython Pathway module.
  • PropertyManager
  • Prosite: This module provides code to work with the prosite dat file from Prosite.
    • Pattern
    • Prodoc: This module provides code to work with the prosite.doc file from Prosite.
  • PubMed: This module provides code to work with PubMed from the NCBI.
  • Rebase: This module provides code to work with files from Rebase.
  • Search
  • Seq
  • SeqFeature: Represent a Sequence Feature holding info about a part of a sequence.
  • SeqIO: Sequence input/output designed to look similar to the bioperl design.
  • SeqRecord
  • Sequencing: Code to deal with various programs for sequencing and assembly.
    • Ace: Parser for (new) ACE files output by PHRAP.
    • Phd: Parser for PHD files output by PHRED and used by PHRAP and CONSED.
  • SGMLExtractor: Code for more fancy file handles.
  • Statistics
    • lowess: This module implements the Lowess function for nonparametric regression.
  • Std
  • StdHandler
  • stringfns: This provides useful general functions for working with strings.
  • SubsMat: Substitution matrices, log odds matrices, and operations on them.
  • SVDSuperimposer: SVDSuperimposer finds the best rotation and translation to put two point sets on top of each other (minimizing the RMSD).
  • SwissProt: Parsers for file formats from the SwissProt database.
    • KeyWList: This module provides code to work with the keywlist.txt file from SwissProt.
    • SProt: This module provides code to work with the sprotXX.dat file from SwissProt.
  • Transcribe
  • Translate
  • triefind: Given a trie, find all occurrences of a word in the trie in a string.
  • UniGene
  • utils
  • Wise
  • Writer
  • writers
  • WWW: Deal with various biological databases and services on the web.
    • ExPASy: This module provides code to access resources at ExPASy over the WWW.
    • InterPro: This module provides code to access resources at InterPro over the WWW.
    • NCBI: Provides code to access NCBI over the WWW.
    • SCOP: Provides code to access SCOP over the WWW.

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