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Bio
: Collection of modules for dealing with biological data in Python.
Affy
: Deal with Affymetrix related data such as cel files.
CelFile
: No version number yet.
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
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.
nlmmedline_001211_format
: A Martel format to parse the NLM's XML format for Medline.
nlmmedline_010319_format
: A Martel format to parse the NLM's XML format for Medline.
nlmmedline_011101_format
: nlmmedline_xml_format.py
nlmmedline_031101_format
: nlmmedline_xml_format.py
NLMMedlineXML
: This module provides code to work the NCBI's XML format for
Medline.
MEME
: Parser for dealing with text output from the MEME motif search
program
Mindy
BaseDB
compression
FlatDB
Location
SimpleSeqRecord
: Index a file based on information in a SeqRecord object.
XPath
MultiProc
: Code to schedule and run multiple processes.
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
Gene
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.
Rep
: BioPython Pathway support module.
PropertyManager
Prosite
: This module provides code to work with the prosite dat 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.
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.
FreqTable
MatrixInfo
: A whole bunch of substitution matrices for use in alignments, etc.
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.
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.
BioSQL
: Code for storing and retrieving biological objects from relational
dbs.
BioSeq
: Implementations of Biopython-like Seq objects on top of BioSQL.
BioSeqDatabase
: Connect with a BioSQL database and load Biopython like objects from
it.
DBUtils
Loader
: Load biopyton objects into a BioSQL database for persistant
storage.
Martel
convert_re
: Converts a regular expression pattern string into an Expression
tree.
Dispatch
Expression
: Classes for nodes in the Expression tree.
formats
Generate
Iterator
: Iterate over records of a XML parse tree.
IterParser
: Implement Martel parsers.
LAX
: A simple way to read lists of fields from flat XML records.
msre_constants
msre_parse
optimize
: Optimize an expression tree...
Parser
: Implement Martel parsers.
RecordReader
test
run_tests
support
test_attrs
test_convert_re
test_delimiter
test_Expression
test_Generate
test_Iterator
test_IterParser
test_LAX
test_macros
test_optimize
test_Parser
test_ParseRecords
test_RecordReader
test_RecordReader2
test_swissprot38
test_Time
testformats
delimiter
: Example of using Martel on a simple delimited file
swissprot38
: Parser for the SWISS-PROT 38 format.
Time
: Parse a time or date string.
Bio.Affy.CelFile.CelParser
:
Takes a handle to an Affymetrix cel file, parses the file and returns
an instance of a CelRecord
Bio.Affy.CelFile.CelRecord
:
Stores the information in a cel file
Bio.Affy.CelFile.CelScanner
:
Scannner for Affymetrix CEL files.
Bio.Ais.Immune
:
friendly should be an instance of Align.
Bio.Ais.Lymphocyte
Bio.Align.AlignInfo.PSSM
:
Represent a position specific score matrix.
Bio.Align.AlignInfo.SummaryInfo
:
Calculate summary info about the alignment.
Bio.Align.FormatConvert.FormatConverter
:
Convert between different alignment representation formats.
Bio.Align.Generic.Alignment
:
Represent a set of alignments.
Bio.AlignAce.Parser.AlignAceConsumer
:
The general purpose consumer for the AlignAceScanner.
Bio.AlignAce.Parser.CompareAceConsumer
:
The general purpose consumer for the CompareAceScanner.
Bio.AlignAce.Scanner.AlignAceScanner
:
Scannner for AlignACE output
Bio.AlignAce.Scanner.CompareAceScanner
:
Scannner for CompareACE output
Bio.Alphabet.Alphabet
Bio.Alphabet.AlphabetEncoder
Bio.Application.AbstractCommandline
:
Generic interface for running applications from biopython.
Bio.AlignAce.Applications.AlignAceCommandline
:
Create a commandline for the AlignAce program.
Bio.Blast.Applications.BlastallCommandline
:
Create a commandline for the blastall program from NCBI.
Bio.AlignAce.Applications.CompareAceCommandline
:
Create a commandline for the CompareAce program.
Bio.Emboss.Applications.EConsenseCommandline
:
Commandline object for the econsense program from EMBOSS.
Bio.Emboss.Applications.EInvertedCommandline
:
Commandline object for the einverted program from EMBOSS.
Bio.Emboss.Applications.ENeighborCommandline
:
Commandline object for the eneighbor program from EMBOSS.
Bio.Emboss.Applications.EProtDistCommandline
:
Commandline object for the eprotdist program from EMBOSS.
Bio.Emboss.Applications.EProtParsCommandline
:
Commandline object for the eprotpars program from EMBOSS.
Bio.Emboss.Applications.ESeqBootCommandline
:
Commandline object for the eseqboot program from EMBOSS.
Bio.Emboss.Applications.Est2GenomeCommandline
:
Commandline object for the est2genome program from EMBOSS.
Bio.Emboss.Applications.ETandemCommandline
:
Commandline object for the etandem program from EMBOSS.
Bio.Blast.Applications.FastacmdCommandline
:
Create a commandline for the fasta program from NCBI.
Bio.Emboss.Applications.FuzznucCommandline
:
Commandline object for the fuzznuc program from EMBOSS.
Bio.Emboss.Applications.PalindromeCommandline
:
Commandline object for the palindrome program from EMBOSS.
Bio.Emboss.Applications.Primer3Commandline
:
Commandline object for the Primer3 interface from EMBOSS.
Bio.Emboss.Applications.PrimerSearchCommandline
:
Commandline object for the primersearch program from EMBOSS.
Bio.Emboss.Applications.TranalignCommandline
:
Commandline object for the tranalign program from EMBOSS.
Bio.Emboss.Applications.WaterCommandline
:
Commandline object for the water program from EMBOSS.
Bio.Application.ApplicationResult
:
Make results of a program available through a standard interface.
Bio.Application._AbstractParameter
:
A class to hold information about a parameter for a commandline.
Bio.Application._Argument
:
Represent an argument on a commandline.
Bio.Application._Option
:
Represent an option that can be set for a program.
Bio.Blast.NCBIStandalone.Iterator
:
Iterates over a file of multiple BLAST results.
Bio.Blast.NCBIStandalone._AlignmentConsumer
Bio.Blast.NCBIStandalone._DatabaseReportConsumer
Bio.Blast.NCBIStandalone._DescriptionConsumer
Bio.Blast.NCBIStandalone._HSPConsumer
Bio.Blast.NCBIStandalone._HeaderConsumer
Bio.Blast.NCBIStandalone._ParametersConsumer
Bio.Blast.NCBIStandalone._Scanner
:
Scan BLAST output from blastall or blastpgp.
Bio.Blast.NCBIWWW._Scanner
:
Scan BLAST output from NCBI's web server at:
http://www.ncbi.nlm.nih.gov/BLAST/
Bio.Blast.ParseBlastTable.BlastTableEntry
Bio.Blast.ParseBlastTable.BlastTableReader
Bio.Blast.ParseBlastTable.BlastTableRec
Bio.Blast.Record.Alignment
:
Stores information about one hit in the alignments section.
Bio.Blast.Record.DatabaseReport
:
Holds information about a database report.
Bio.Blast.Record.Blast
:
Saves the results from a blast search.
Bio.Blast.Record.PSIBlast
:
Saves the results from a blastpgp search.
Bio.Blast.Record.Description
:
Stores information about one hit in the descriptions section.
Bio.Blast.Record.HSP
:
Stores information about one hsp in an alignment hit.
Bio.Blast.Record.Header
:
Saves information from a blast header.
Bio.Blast.Record.Blast
:
Saves the results from a blast search.
Bio.Blast.Record.PSIBlast
:
Saves the results from a blastpgp search.
Bio.Blast.Record.MultipleAlignment
:
Holds information about a multiple alignment.
Bio.Blast.Record.Parameters
:
Holds information about the parameters.
Bio.Blast.Record.Blast
:
Saves the results from a blast search.
Bio.Blast.Record.PSIBlast
:
Saves the results from a blastpgp search.
Bio.Blast.Record.Round
:
Holds information from a PSI-BLAST round.
Bio.CAPS.CAPSMap
:
A map of an alignment showing all possible dcuts.
Bio.CAPS.DifferentialCutsite
:
A differential cutsite is a location in an alignment where an enzyme cuts
at least one sequence and also cannot cut at least one other sequence.
Bio.Compass.Iterator
:
Iterate through a file of compass results
Bio.Compass.Record
:
Hold information from one compass hit.
Bio.Compass._Consumer
Bio.Compass._Scanner
:
Reads compass output and generate events
Bio.Crystal.Chain
Bio.Crystal.Crystal
Bio.Crystal.Hetero
:
This class exists to support the PDB hetero codes.
Bio.DBXRef.BioformatDBName
Bio.DBXRef.DBXRef
Bio.DBXRef.UnknownDBName
Bio.Data.CodonTable.AmbiguousForwardTable
Bio.Data.CodonTable.CodonTable
Bio.Decode.Function
Bio.Decode.FunctionCall
Bio.Decode.FunctionCallChain
Bio.Decode.Token
Bio.EUtils.Config.DatabaseInfo
:
stores NCBI's name for the database and its type
Bio.EUtils.DBIdsClient.DBIdsClient
:
Create a RecordSet either from a search or a set of dbids
Bio.EUtils.DBIdsClient.PublicationDBIdsFetchMixin
:
Support 'efetch' for publication records
Bio.EUtils.DBIdsClient.PublicationDBIdsRecord
:
a single publication record, referenced by database identifier
Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet
:
a set of publication records, referenced by database identifier
Bio.EUtils.DBIdsClient.SequenceDBIdsFetchMixin
:
Support 'efetch' for sequence records
Bio.EUtils.DBIdsClient.SequenceDBIdsRecord
:
a single sequence record, referenced by database identifier
Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet
:
a set of sequence records, referenced by database identifier
Bio.EUtils.Datatypes.DBIds
:
Store a list of identifiers for a database
Bio.EUtils.Datatypes.Date
:
Allow simple Date storage
Bio.EUtils.Datatypes.DateRange
:
Restrict a search to matches within a date range...
Bio.EUtils.Datatypes.Expression
:
Base class for the Expression given in the eSearch output
Bio.EUtils.Datatypes.BinaryOp
:
Base class for binary expressions.
Bio.EUtils.Datatypes.And
:
intersection of two subexpressions
Bio.EUtils.Datatypes.Not
:
the set of the left child without elements from the right child
Bio.EUtils.Datatypes.Or
:
union two subexpressions
Bio.EUtils.Datatypes.Range
:
Used to store a date range
Bio.EUtils.Datatypes.Term
:
Information about an Expression Term, which is the leaf node...
Bio.EUtils.Datatypes.IdCheck
:
Store results from an lcheck link...
Bio.EUtils.Datatypes.IdUrlSet
:
Set of ObjUrls for the record with the given 'id'
Bio.EUtils.Datatypes.Link
:
Store neighbor Link information for a given record...
Bio.EUtils.Datatypes.LinksLinkSet
:
Results of an 'llink' (LinkOut) search
Finds links from records in a given database to external
resources.
Bio.EUtils.Datatypes.NeighborLinkSet
:
Results from an eLink neighbor search...
Bio.EUtils.Datatypes.ObjUrl
:
The ObjUrl containing LinkOut information for a record...
Bio.EUtils.Datatypes.PostResult
:
Store the results of a Post
Attributes are:
webenv -- the WebEnv string
query_key -- the query_ket
timestamp -- timestamp (from time.time()) when this record
was received from the server.
Bio.EUtils.Datatypes.Problem
:
Base class for Search Errors or Warnings...
Bio.EUtils.Datatypes.Provider
:
The Provider, as listed in 'llinks' (LinkOut)...
Bio.EUtils.Datatypes.SearchResult
:
Store results from a database search
Attributes are:
count -- total number of matches to the query
retmax -- total number of identifiers requested
retstart -- a search can return a portion of the total
number of results.
Bio.EUtils.Datatypes.Summary
:
Store information from calling eSummary
Attributes are:
id -- the identifier string for this record
dataitems -- an OrderedDictList containing the parsed Item
elements for this Summary.
Bio.EUtils.Datatypes.WithinNDays
:
Restrict a search to matches in the last N days
Bio.EUtils.HistoryClient.HistoryClient
Bio.EUtils.HistoryClient.HistoryCookie
:
Data needed to get back to the history
Bio.EUtils.HistoryClient.PublicationHistoryFetchMixin
Bio.EUtils.HistoryClient.SequenceHistoryFetchMixin
Bio.EUtils.Mixins.LinkMixin
Bio.EUtils.Mixins.PublicationFetchMixin
Bio.EUtils.DBIdsClient.PublicationDBIdsRecord
:
a single publication record, referenced by database identifier
Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet
:
a set of publication records, referenced by database identifier
Bio.EUtils.HistoryClient.PublicationHistoryRecord
Bio.EUtils.HistoryClient.PublicationHistoryRecordSet
Bio.EUtils.Mixins.SequenceFetchMixin
Bio.EUtils.DBIdsClient.SequenceDBIdsRecord
:
a single sequence record, referenced by database identifier
Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet
:
a set of sequence records, referenced by database identifier
Bio.EUtils.HistoryClient.SequenceHistoryRecord
Bio.EUtils.HistoryClient.SequenceHistoryRecordSet
Bio.EUtils.MultiDict._BaseMultiDict
Bio.EUtils.MultiDict.OrderedMultiDict
:
Store key/value mappings.
Bio.EUtils.MultiDict.UnorderedMultiDict
:
Store key/value mappings.
Bio.EUtils.POM.ContentModel
:
Represents and validates a content model.
Bio.EUtils.POM.DTDConsumerForSourceGeneration
Bio.EUtils.POM.ElementNode
Bio.EUtils.DTDs.LinkOut.apad
Bio.EUtils.DTDs.LinkOut.Attribute
Bio.EUtils.DTDs.eLink_020511.Attribute
Bio.EUtils.DTDs.LinkOut.Base
Bio.EUtils.DTDs.LinkOut.Brief
Bio.EUtils.DTDs.eInfo_020511.Count
Bio.EUtils.DTDs.eSearch_020511.Count
Bio.EUtils.DTDs.LinkOut.Database
Bio.EUtils.DTDs.eLink_020511.DbFrom
Bio.EUtils.DTDs.eInfo_020511.DbInfo
Bio.EUtils.DTDs.eInfo_020511.DbList
Bio.EUtils.DTDs.eInfo_020511.DbName
Bio.EUtils.DTDs.eInfo_020511.DbTo
Bio.EUtils.DTDs.eLink_020511.DbTo
Bio.EUtils.DTDs.eInfo_020511.Descriptor
Bio.EUtils.DTDs.eSummary_020511.DocSum
Bio.EUtils.DTDs.eInfo_020511.eInfoResult
Bio.EUtils.DTDs.eLink_020511.eLinkResult
Bio.EUtils.DTDs.ePost_020511.ePostResult
Bio.EUtils.DTDs.eInfo_020511.ERROR
Bio.EUtils.DTDs.eLink_020511.ERROR
Bio.EUtils.DTDs.ePost_020511.ERROR
Bio.EUtils.DTDs.eSearch_020511.ERROR
Bio.EUtils.DTDs.eSummary_020511.ERROR
Bio.EUtils.DTDs.eSearch_020511.ErrorList
Bio.EUtils.DTDs.eSearch_020511.eSearchResult
Bio.EUtils.DTDs.eSummary_020511.eSummaryResult
Bio.EUtils.DTDs.LinkOut.ExclQuery
Bio.EUtils.DTDs.eSearch_020511.Explode
Bio.EUtils.DTDs.eInfo_020511.Field
Bio.EUtils.DTDs.eSearch_020511.Field
Bio.EUtils.DTDs.eSearch_020511.FieldNotFound
Bio.EUtils.DTDs.eInfo_020511.FiledList
Bio.EUtils.POM.Fragments
:
Fragments is a special holder class to hold 'loose' markup
fragments.
Bio.EUtils.DTDs.eSearch_020511.From
Bio.EUtils.DTDs.eInfo_020511.Hierarchy
Bio.EUtils.DTDs.LinkOut.IconUrl
Bio.EUtils.DTDs.eLink_020511.IconUrl
Bio.EUtils.DTDs.eLink_020511.Id
Bio.EUtils.DTDs.ePost_020511.Id
Bio.EUtils.DTDs.eSearch_020511.Id
Bio.EUtils.DTDs.eSummary_020511.Id
Bio.EUtils.DTDs.eLink_020511.IdCheckList
Bio.EUtils.DTDs.eLink_020511.IdList
Bio.EUtils.DTDs.eSearch_020511.IdList
Bio.EUtils.DTDs.eLink_020511.IdUrlList
Bio.EUtils.DTDs.eLink_020511.IdUrlSet
Bio.EUtils.DTDs.LinkOut.InclQuery
Bio.EUtils.DTDs.eLink_020511.Info
Bio.EUtils.DTDs.ePost_020511.InvalidIdList
Bio.EUtils.DTDs.eInfo_020511.IsDate
Bio.EUtils.DTDs.eInfo_020511.IsNumerical
Bio.EUtils.DTDs.eSummary_020511.Item
Bio.EUtils.DTDs.LinkOut.Link
Bio.EUtils.DTDs.eInfo_020511.Link
Bio.EUtils.DTDs.eLink_020511.Link
Bio.EUtils.DTDs.LinkOut.LinkId
Bio.EUtils.DTDs.eInfo_020511.LinkList
Bio.EUtils.DTDs.eLink_020511.LinkName
Bio.EUtils.DTDs.LinkOut.LinkSet
Bio.EUtils.DTDs.eLink_020511.LinkSet
Bio.EUtils.DTDs.eLink_020511.LinkSetDb
Bio.EUtils.DTDs.eInfo_020511.Menu
Bio.EUtils.DTDs.eInfo_020511.MenuName
Bio.EUtils.DTDs.LinkOut.Name
Bio.EUtils.DTDs.eInfo_020511.Name
Bio.EUtils.DTDs.eLink_020511.Name
Bio.EUtils.DTDs.LinkOut.NameAbbr
Bio.EUtils.DTDs.eLink_020511.NameAbbr
Bio.EUtils.DTDs.LinkOut.normalize
Bio.EUtils.DTDs.LinkOut.ObjectList
Bio.EUtils.DTDs.LinkOut.ObjectSelector
Bio.EUtils.DTDs.LinkOut.ObjectUrl
Bio.EUtils.DTDs.LinkOut.ObjId
Bio.EUtils.DTDs.eLink_020511.ObjUrl
Bio.EUtils.DTDs.eSearch_020511.OP
Bio.EUtils.DTDs.eSearch_020511.OutputMessage
Bio.EUtils.DTDs.LinkOut.pad
Bio.EUtils.DTDs.eSearch_020511.PhraseIgnored
Bio.EUtils.DTDs.eSearch_020511.PhraseNotFound
Bio.EUtils.DTDs.LinkOut.Provider
Bio.EUtils.DTDs.eLink_020511.Provider
Bio.EUtils.DTDs.LinkOut.ProviderId
Bio.EUtils.DTDs.LinkOut.Query
Bio.EUtils.DTDs.ePost_020511.QueryKey
Bio.EUtils.DTDs.eSearch_020511.QueryKey
Bio.EUtils.DTDs.eSearch_020511.QueryTranslation
Bio.EUtils.DTDs.eSearch_020511.QuotedPhraseNotFound
Bio.EUtils.DTDs.eSearch_020511.RetMax
Bio.EUtils.DTDs.eSearch_020511.RetStart
Bio.EUtils.DTDs.LinkOut.Rule
Bio.EUtils.DTDs.LinkOut.RuleToMany
Bio.EUtils.DTDs.eLink_020511.Score
Bio.EUtils.DTDs.LinkOut.Separator
Bio.EUtils.DTDs.eInfo_020511.SingleToken
Bio.EUtils.DTDs.LinkOut.strip
Bio.EUtils.DTDs.LinkOut.SubjectType
Bio.EUtils.DTDs.eLink_020511.SubjectType
Bio.EUtils.DTDs.LinkOut.SubObjectSelector
Bio.EUtils.DTDs.LinkOut.SubProvider
Bio.EUtils.DTDs.LinkOut.subs
Bio.EUtils.DTDs.eSearch_020511.Term
Bio.EUtils.DTDs.eInfo_020511.TermCount
Bio.EUtils.DTDs.eSearch_020511.TermSet
Bio.EUtils.DTDs.eSearch_020511.To
Bio.EUtils.DTDs.LinkOut.tolower
Bio.EUtils.DTDs.LinkOut.toupper
Bio.EUtils.DTDs.eSearch_020511.Translation
Bio.EUtils.DTDs.eSearch_020511.TranslationSet
Bio.EUtils.DTDs.eSearch_020511.TranslationStack
Bio.EUtils.DTDs.LinkOut.Url
Bio.EUtils.DTDs.eLink_020511.Url
Bio.EUtils.DTDs.LinkOut.UrlName
Bio.EUtils.DTDs.eSearch_020511.WarningList
Bio.EUtils.DTDs.ePost_020511.WebEnv
Bio.EUtils.DTDs.eSearch_020511.WebEnv
Bio.EUtils.POM.ObjectParserHandler
Bio.EUtils.POM.POMDocument
Bio.EUtils.POM.XMLAttribute
Bio.EUtils.POM._ContentModelGenerator
:
_ContentModelGenerator(rawmodel) The DTD parser generated and final
content model are so different that a different content model generator
is used for this object.
Bio.EUtils.ReseekFile.ReseekFile
:
wrap a file handle to allow seeks back to the beginning
Bio.EUtils.ThinClient.ThinClient
:
Client-side interface to the EUtils services
Bio.EUtils.parse.GetObject
Bio.EUtils.parse.UsePOMParser
Bio.EUtils.sourcegen.ClassHolder
Bio.EUtils.sourcegen.FunctionHolder
Bio.EUtils.sourcegen.MethodHolder
Bio.EUtils.sourcegen.SourceFile
Bio.EUtils.sourcegen.SourceGen
:
SourceGen(outfile, [bangline]) An instance of this SourceGen class is
a factory for generating python source code, by writing to a file
object.
Bio.Emboss.Primer.Primer3Parser
:
Parse primer3 output into a Primer3Record.
Bio.Emboss.Primer.Primer3Primers
:
A primer set designed by Primer3.
Bio.Emboss.Primer.Primer3Record
:
Represent information from a primer3 run finding primers.
Bio.Emboss.Primer.PrimerSearchAmplifier
:
Represent a single amplification from a primer.
Bio.Emboss.Primer.PrimerSearchInputRecord
:
Represent the input file into the primersearch program.
Bio.Emboss.Primer.PrimerSearchOutputRecord
:
Represent the information from a primersearch job.
Bio.Emboss.Primer.PrimerSearchParser
:
Parse primersearch output into a PrimerSearchOutputRecord.
Bio.Emboss.Primer._Primer3Scanner
:
Scan output from the primer3 program.
Bio.Emboss.Primer._PrimerSearchScanner
:
Scan output from the primersearch program.
Bio.Enzyme.DataRecord
Bio.Enzyme.EnzymeRecord
Bio.Enzyme.Iterator
Bio.Enzyme._Scanner
:
Scans Enzyme data.
Bio.FSSP.FSSPAlignRec
Bio.FSSP.FSSPHeader
Bio.FSSP.FSSPSumRec
:
Contains info from an FSSP summary record
Bio.FSSP.PosAlign
Bio.FSSP.fssp_rec.align
Bio.FSSP.fssp_rec.fff_rec
Bio.File.SGMLHandle
:
A Python handle that automatically strips SGML tags from data.
Bio.File.SGMLStripper
Bio.File.UndoHandle
:
A Python handle that adds functionality for saving lines.
Bio.FilteredReader.FilteredReader
Bio.FormatIO.FormatIO
Bio.FormatIO.FormatIOIterator
Bio.GA.Crossover.General.SafeFitnessCrossover
:
Perform crossovers, but do not allow decreases in organism
fitness.
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover
:
Perform n-point crossover between genomes at some defined rates.
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover
:
Demonstration class for Interleaving crossover
Bio.GA.Crossover.GeneralPoint.TwoCrossover
:
Helper class for Two Point crossovers
Bio.GA.Crossover.Point.SinglePointCrossover
:
Perform point crossover between genomes at some defined rate.
Bio.GA.Crossover.TwoPoint.TwoPointCrossover
:
Perform two point crossover between genomes at some defined rate.
Bio.GA.Crossover.Uniform.UniformCrossover
:
Perform single point crossover between genomes at some defined
rates.
Bio.GA.Evolver.GenerationEvolver
:
Evolve a population from generation to generation.
Bio.GA.Evolver.SteadyStateEvolver
:
Evolve a population in place.
Bio.GA.Mutation.General.SafeFitnessMutation
:
Perform mutations, but do not allow decreases in organism fitness.
Bio.GA.Mutation.Simple.ConversionMutation
:
Potentially mutate any item to another in the alphabet.
Bio.GA.Mutation.Simple.SinglePositionMutation
:
Perform a conversion mutation, but only at a single point in the
genome.
Bio.GA.Organism.Organism
:
Represent a single individual in a population.
Bio.GA.Repair.Stabilizing.AmbiguousRepair
:
Perform repair to reduce the number of Ambiguous genes in a
genome.
Bio.GA.Selection.Abstract.AbstractSelection
:
Base class for Selector classes.
Bio.GA.Selection.Diversity.DiversitySelection
:
Implement diversity selection.
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection
:
Roulette wheel selection proportional to individuals fitness.
Bio.GA.Selection.Tournament.TournamentSelection
:
Implement tournament style selection.
Bio.Gobase.Dictionary
:
Accesses a gobase file using a dictionary interface.
Bio.Gobase.Iterator
:
Returns one record at a time from a Gobase file.
Bio.Gobase.Record
:
Holds information from a Gobase record.
Bio.Gobase.GeneRecord
:
Holds information from a Gobase record.
Bio.Gobase.ProteinRecord
:
Holds information from a Gobase record.
Bio.Gobase.SequenceRecord
:
Holds information from a Gobase record.
Bio.Gobase.RecordParser
:
Parses Gobase sequence data into a Record object.
Bio.Gobase._Scanner
:
Scans a gobase file.
Bio.Graphics.Comparative.ComparativeScatterPlot
:
Display a scatter-type plot comparing two different kinds of info.
Bio.Graphics.DisplayRepresentation.ChromosomeCounts
:
Represent a chromosome with count information.
Bio.Graphics.Distribution.BarChartDistribution
:
Display the distribution of values as a bunch of bars.
Bio.Graphics.Distribution.DistributionPage
:
Display a grouping of distributions on a page.
Bio.Graphics.Distribution.LineDistribution
:
Display the distribution of values as connected lines.
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms
:
An abstract class to calculate forward and backward probabiliies.
Bio.HMM.DynamicProgramming.LogDPAlgorithms
:
Implement forward and backward algorithms using a log approach.
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms
:
Implement forward and backward algorithms using a rescaling
approach.
Bio.HMM.MarkovModel.HiddenMarkovModel
:
Represent a hidden markov model that can be used for state
estimation.
Bio.HMM.MarkovModel.MarkovModelBuilder
:
Interface to build up a Markov Model.
Bio.HMM.Trainer.AbstractTrainer
:
Provide generic functionality needed in all trainers.
Bio.HMM.Trainer.BaumWelchTrainer
:
Trainer that uses the Baum-Welch algorithm to estimate parameters.
Bio.HMM.Trainer.KnownStateTrainer
:
Estimate probabilities with known state sequences.
Bio.HMM.Trainer.TrainingSequence
:
Hold a training sequence with emissions and optionally, a state
path.
Bio.HotRand.HotCache
Bio.HotRand.HotRandom
Bio.LogisticRegression.LogisticRegression
:
Holds information necessary to do logistic regression
classification.
Bio.MEME.Motif.Instance
:
A class describing the instances of a motif, and the data thereof.
Bio.MEME.Motif.Motif
:
A generic motif class.
Bio.MEME.Motif.MEMEMotif
:
A subclass of Motif used in parsing MEME (and MAST) output.
Bio.MEME.Parser.MASTRecord
:
The class for holding the results from a MAST run.
Bio.MEME.Parser.MEMERecord
:
A class for holding the results of a MEME run.
Bio.MEME.Parser._MASTConsumer
:
Consumer that can receive events from _MASTScanner.
Bio.MEME.Parser._MASTScanner
:
Scanner for MAST text output.
Bio.MEME.Parser._MEMEConsumer
:
Consumer that can receive events from MEME Scanner.
Bio.MEME.Parser._MEMEScanner
:
Scanner for MEME output.
Bio.MarkovModel.MarkovModel
Bio.MarkupEditor.MarkupEditor
Bio.MarkupEditor.MidPoint
Bio.MaxEntropy.MaxEntropy
:
Holds information for a Maximum Entropy classifier.
Bio.Medline.Iterator
:
Returns one record at a time from a file of Medline records.
Bio.Medline.NLMMedlineXML.Citation
:
Holds information about a Medline citation.
Bio.Medline.NLMMedlineXML._SavedDataHandle
Bio.Medline.Record
:
Holds information from a Medline record.
Bio.Medline._Scanner
:
Scans a Medline record.
Bio.Mindy.BaseDB.DictLookup
Bio.Mindy.BaseDB.WriteDB
Bio.Mindy.FlatDB.BisectFile
Bio.Mindy.Location.Location
:
Handle for a record (use 'text' to get the record's text)
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer
:
Base class for indexing using SeqRecord information.
Bio.Mindy.SimpleSeqRecord.FunctionIndexer
:
Indexer to index based on values returned by a function.
Bio.Mindy.SimpleSeqRecord.SimpleIndexer
:
Index a file based on .id and .name attributes of a SeqRecord.
Bio.MultiProc.Scheduler.Scheduler
:
Schedules threads to be run.
Bio.MultiProc.Task.Task
:
Contains information for one process.
Bio.MultiProc.copen._PickleHandle
:
Members: pid what is the PID of the subprocess? killsig what signal
killed the child process? status what was the status of the command?
Bio.MultiProc.copen._ProcHandle
:
This object provides a file-like interface to a running process.
Bio.NMR.xpktools.Peaklist
Bio.NMR.xpktools.XpkEntry
Bio.NaiveBayes.NaiveBayes
:
Holds information for a NaiveBayes classifier.
Bio.NetCatch.NetCatch
:
Decorator for a dictionary of links.
Bio.NetCatch.Url
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer
:
Abstract base class for all layers.
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork
:
Represent a Basic Neural Network with three layers.
Bio.NeuralNetwork.Gene.Motif.MotifCoder
:
Convert motifs and a sequence into neural network representations.
Bio.NeuralNetwork.Gene.Motif.MotifFinder
:
Find motifs in a set of Sequence Records.
Bio.NeuralNetwork.Gene.Pattern.PatternIO
:
Allow reading and writing of patterns to files.
Bio.NeuralNetwork.Gene.Pattern.PatternRepository
:
This holds a list of specific patterns found in sequences.
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness
:
Calculate fitness for schemas that differentiate between
sequences.
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder
:
Find schemas using a genetic algorithm approach.
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness
:
Calculate a fitness giving weight to schemas that match many
times.
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator
:
Generate a random motif within given parameters.
Bio.NeuralNetwork.Gene.Schema.Schema
:
Deal with motifs that have ambiguity characters in it.
Bio.NeuralNetwork.Gene.Schema.SchemaCoder
:
Convert a sequence into a representation of ambiguous motifs
(schemas).
Bio.NeuralNetwork.Gene.Schema.SchemaFactory
:
Generate Schema from inputs of Motifs or Signatures.
Bio.NeuralNetwork.Gene.Schema.SchemaFinder
:
Find schema in a set of sequences using a genetic algorithm
approach.
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher
:
Determine when we are done evolving motifs.
Bio.NeuralNetwork.Gene.Signature.SignatureCoder
:
Convert a Sequence into its signature representatives.
Bio.NeuralNetwork.Gene.Signature.SignatureFinder
:
Find Signatures in a group of sequence records.
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop
:
Class to stop training on a network when the validation error
increases.
Bio.NeuralNetwork.Training.ExampleManager
:
Manage a grouping of Training Examples.
Bio.NeuralNetwork.Training.TrainingExample
:
Hold inputs and outputs of a training example.
Bio.Nexus.Nexus.Block
:
Represent a NEXUS block with block name and list of commandlines .
Bio.Nexus.Nexus.CharBuffer
:
Helps reading NEXUS-words and characters from a buffer.
Bio.Nexus.Nexus.Commandline
:
Represent a commandline as command and options.
Bio.Nexus.Nexus.StepMatrix
:
Calculate a stepmatrix for weighted parsimony.
Bio.Nexus.Nodes.Chain
:
Stores a list of nodes that are linked together.
Bio.Nexus.Trees.Tree
:
Represents a tree using a chain of nodes with on predecessor
(=ancestor) and multiple successors (=subclades).
Bio.Nexus.Nodes.Node
:
A single node.
Bio.Nexus.Trees.NodeData
:
Stores tree-relevant data associated with nodes (e.g.
Bio.ParserSupport.AbstractConsumer
:
Base class for other Consumers.
Bio.Affy.CelFile.CelConsumer
Bio.ParserSupport.TaggingConsumer
:
A Consumer that tags the data stream with the event and prints it to a
handle.
Bio.Blast.NCBIStandalone._BlastConsumer
Bio.SwissProt.KeyWList._ListConsumer
:
Consumer that converts a keywlist.txt file into a list of
keywords.
Bio.Emboss.Primer._Primer3RecordConsumer
:
Get output from prime3 into a Primer3Record
Bio.Emboss.Primer._PrimerSearchRecordConsumer
:
Get output from primersearch into a PrimerSearchOutputRecord
Bio.Blast.NCBIStandalone._PSIBlastConsumer
Bio.Enzyme._RecordConsumer
Bio.Gobase._RecordConsumer
:
Consumer that converts a gobase record to a Record object.
Bio.Medline._RecordConsumer
:
Consumer that converts a Medline record to a Record object.
Bio.Prosite.Prodoc._RecordConsumer
:
Consumer that converts a Prodoc record to a Record object.
Bio.Prosite._RecordConsumer
:
Consumer that converts a Prosite record to a Record object.
Bio.Rebase._RecordConsumer
:
Consumer that converts a rebase record to a Record object.
Bio.Sequencing.Ace._RecordConsumer
:
Reads the ace tags into data records.
Bio.Sequencing.Phd._RecordConsumer
:
Consumer that converts a PHD record to a Record object
Bio.SwissProt.SProt._RecordConsumer
:
Consumer that converts a SwissProt record to a Record object.
Bio.SwissProt.SProt._SequenceConsumer
:
Consumer that converts a SwissProt record to a SeqRecord object.
Bio.ParserSupport.AbstractParser
:
Base class for other parsers.
Bio.Sequencing.Ace.ACEParser
:
Parses full ACE file in list of contigs.
Bio.AlignAce.Parser.AlignAceParser
:
Parses AlignAce data into a sequence of Motifs.
Bio.Blast.NCBIStandalone.BlastErrorParser
:
Attempt to catch and diagnose BLAST errors while parsing.
Bio.Blast.NCBIStandalone.BlastParser
:
Parses BLAST data into a Record.Blast object.
Bio.Blast.NCBIWWW.BlastParser
:
Parses WWW BLAST data into a Record.Blast object.
Bio.Medline.NLMMedlineXML.CitationParser
:
Parses a citation into a Record object.
Bio.AlignAce.Parser.CompareAceParser
:
Parses CompareAce output to usable form
Bio.SwissProt.KeyWList.ListParser
:
Parses keywlist.txt data into a list of keywords.
Bio.MEME.Parser.MASTParser
:
Parser for MAST text output.
Bio.MEME.Parser.MEMEParser
:
A parser for the text output of the MEME program.
Bio.Blast.NCBIStandalone.PSIBlastParser
:
Parses BLAST data into a Record.PSIBlast object.
Bio.Compass.RecordParser
:
Parses compass results into a Record object.
Bio.Enzyme.RecordParser
Bio.Medline.RecordParser
:
Parses Medline data into a Record object.
Bio.Prosite.Prodoc.RecordParser
:
Parses Prodoc data into a Record object.
Bio.Prosite.RecordParser
:
Parses Prosite data into a Record object.
Bio.Sequencing.Ace.RecordParser
:
Parses ACE file data into a Record object
Bio.Sequencing.Phd.RecordParser
:
Parses PHD file data into a Record object
Bio.SwissProt.SProt.RecordParser
:
Parses SwissProt data into a Record object.
Bio.SwissProt.SProt.SequenceParser
:
Parses SwissProt data into a standard SeqRecord object.
Bio.ParserSupport.SGMLStrippingConsumer
:
A consumer that strips off SGML tags.
Bio.Parsers.spark.GenericASTTraversal
Bio.Parsers.spark.GenericASTTraversalPruningException
Bio.Parsers.spark.GenericParser
Bio.Parsers.spark.GenericScanner
Bio.Pathway.Interaction
:
An arbitrary interaction between any number of species.
Bio.Pathway.Network
:
A set of species that are explicitly linked by interactions.
Bio.Pathway.Reaction
:
Abstraction for a biochemical transformation.
Bio.Pathway.Rep.Graph.Graph
:
A directed graph abstraction with labeled edges.
Bio.Pathway.Rep.HashSet.HashSet
:
A set abstraction supporting the basic set operations.
Bio.Pathway.Rep.MultiGraph.MultiGraph
:
A directed multigraph abstraction with labeled edges.
Bio.Pathway.System
:
Abstraction for a collection of reactions.
Bio.PropertyManager.PropertyManager
Bio.Prosite.Dictionary
:
Accesses a Prosite file using a dictionary interface.
Bio.Prosite.ExPASyDictionary
:
Access PROSITE at ExPASy using a read-only dictionary interface.
Bio.Prosite.Iterator
:
Returns one record at a time from a Prosite file.
Bio.Prosite.Pattern.Prosite
Bio.Prosite.Pattern.PrositeMatch
Bio.Prosite.Pattern.PrositeTerm
Bio.Prosite.PatternHit
:
Holds information from a hit against a Prosite pattern.
Bio.Prosite.Prodoc.Dictionary
:
Accesses a Prodoc file using a dictionary interface.
Bio.Prosite.Prodoc.ExPASyDictionary
:
Access PRODOC at ExPASy using a read-only dictionary interface.
Bio.Prosite.Prodoc.Iterator
:
Returns one record at a time from a Prodoc file.
Bio.Prosite.Prodoc.Record
:
Holds information from a Prodoc record.
Bio.Prosite.Prodoc.Reference
:
Holds information from a Prodoc citation.
Bio.Prosite.Prodoc._Scanner
:
Scans Prodoc-formatted data.
Bio.Prosite.Record
:
Holds information from a Prosite record.
Bio.Prosite._Scanner
:
Scans Prosite-formatted data.
Bio.PubMed.Dictionary
:
Access PubMed using a read-only dictionary interface.
Bio.Rebase.Dictionary
:
Accesses a rebase file using a dictionary interface.
Bio.Rebase.Iterator
:
Returns one record at a time from a Rebase file.
Bio.Rebase.Record
:
Holds information from a FASTA record.
Bio.Rebase.RecordParser
:
Parses FASTA sequence data into a Record object.
Bio.Rebase._Scanner
:
Scans a rebase file.
Bio.SGMLExtractor.SGMLExtractor
Bio.SGMLExtractor.SGMLExtractorHandle
:
A Python handle that automatically strips SGML tags and returns data
from specified tag start and end pairs.
Bio.SVDSuperimposer.SVDSuperimposer.SVDSuperimposer
:
SVDSuperimposer finds the best rotation and translation to put two
point sets on top of each other (minimizing the RMSD).
Bio.Search.Algorithm
Bio.Search.Database
Bio.Search.Hit
Bio.Search.Query
Bio.Search.Search
Bio.Search.TableInfo
Bio.Search._SeqLength
Bio.Seq.MutableSeq
Bio.Seq.Seq
Bio.SeqFeature.AbstractPosition
:
Abstract base class representing a position.
Bio.SeqFeature.AfterPosition
:
Specify a position where the actual location is found after it.
Bio.SeqFeature.BeforePosition
:
Specify a position where the actual location occurs before it.
Bio.SeqFeature.BetweenPosition
:
Specify the position of a boundary between two coordinates.
Bio.SeqFeature.ExactPosition
:
Specify the specific position of a boundary.
Bio.SeqFeature.OneOfPosition
:
Specify a position where the location can be multiple positions.
Bio.SeqFeature.WithinPosition
:
Specify the position of a boundary within some coordinates.
Bio.SeqFeature.FeatureLocation
:
Specify the location of a feature along a sequence.
Bio.SeqFeature.PositionGap
:
Simple class to hold information about a gap between positions.
Bio.SeqFeature.Reference
:
Represent a Generic Reference object.
Bio.SeqFeature.SeqFeature
:
Represent a Sequence Feature on an object.
Bio.SeqIO.FASTA.FastaReader
Bio.SeqIO.FASTA.FastaWriter
Bio.SeqIO.generic.GenericFormat
Bio.SeqIO.generic.ReadSeq
Bio.SeqIO.generic.SeqRecord
Bio.SeqRecord.SeqRecord
Bio.Sequencing.Ace.ACEFileRecord
:
Holds data of ACE file.
Bio.Sequencing.Ace.Contig
:
Hold information from a ACE record
Bio.Sequencing.Ace.Iterator
:
Iterates over a ACE-file with multiple contigs
Bio.Sequencing.Ace.Reads
Bio.Sequencing.Ace._Scanner
:
Scans a ACE-formatted file
Bio.Sequencing.Ace.af
Bio.Sequencing.Ace.bs
Bio.Sequencing.Ace.ct
Bio.Sequencing.Ace.ds
Bio.Sequencing.Ace.qa
Bio.Sequencing.Ace.rd
Bio.Sequencing.Ace.rt
Bio.Sequencing.Ace.wa
Bio.Sequencing.Ace.wr
Bio.Sequencing.Phd.Iterator
:
Iterates over a file of multiple PHD records
Bio.Sequencing.Phd.Record
:
Hold information from a PHD file
Bio.Sequencing.Phd._Scanner
:
Scans a PHD-formatted file
Bio.StdHandler.Feature
Bio.SwissProt.KeyWList._Scanner
:
Scan the keywlist.txt file included with the SwissProt
distribution.
Bio.SwissProt.SProt.Dictionary
:
Accesses a SwissProt file using a dictionary interface.
Bio.SwissProt.SProt.ExPASyDictionary
:
Access SwissProt at ExPASy using a read-only dictionary interface.
Bio.SwissProt.SProt.Iterator
:
Returns one record at a time from a SwissProt file.
Bio.SwissProt.SProt.Record
:
Holds information from a SwissProt record.
Bio.SwissProt.SProt.Reference
:
Holds information from 1 references in a SwissProt entry.
Bio.SwissProt.SProt._Scanner
:
Scans SwissProt-formatted data.
Bio.Transcribe.Transcribe
Bio.Translate.Translator
Bio.WWW.RequestLimiter
Bio.Writer.Writer
Bio.config.DBRegistry.TextLikeMixin
:
Mixin class with useful functionality for retrival of text files.
Bio.config.DBRegistry.CGIDB
:
This class implements DBObject for accessing CGI databases.
Bio.config.DBRegistry.EUtilsDB
:
Implement DBObject for accessing EUtils databases at NCBI.
Bio.config.Registry.RegisterableObject
:
This is a base class for objects that can be added to a registry.
Bio.config.DBRegistry.DBObject
:
This is a base class for dictionary-like interfaces to
databases.
Bio.config.DBRegistry.BioCorbaDB
:
Represent a BioCorba BioSequenceCollection for SeqRecord objects.
Bio.config.DBRegistry.BioSQLDB
:
Represent a BioSQL-style database to retrieve SeqRecord objects.
Bio.config.DBRegistry.CGIDB
:
This class implements DBObject for accessing CGI databases.
Bio.config.DBRegistry.EUtilsDB
:
Implement DBObject for accessing EUtils databases at NCBI.
Bio.config.DBRegistry.IndexedFileDB
:
Return SeqRecord objects from an indexed file.
Bio.config.FormatRegistry.FormatObject
:
This object stores Biopython file formats and provides methods to work
on them.
Bio.config.Registry.RegisterableGroup
:
This is a base class for a RegisterableObject that groups many objects
together.
Bio.config.DBRegistry.DBGroup
:
Groups DBObjects that return the same kind of data.
Bio.config.FormatRegistry.FormatGroup
:
This object holds a group of FormatObjects.
Bio.config.Registry.Registry
:
This is a dictionary-like object for storing and retrieving
objects in a registry.
Bio.config.DBRegistry.DBRegistry
:
This implements a dictionary-like interface to databases.
Bio.config.SeqDBRegistry.SeqDBRegistry
:
This object implements a dictionary-like interface to sequence
databases.
Bio.config.FormatRegistry.FormatRegistry
:
This implements a dictionary-like interface to Biopython file
formats.
Bio.config._stanzaformat.Stanza
:
Contains information about one stanza in a file.
Bio.config._stanzaformat.StanzaFormat
:
Contains information from a stanza-formatted file.
Bio.config._support.make_cached_expression
:
make_cached_expression(expression) -> cached expression object
Bio.config._support.make_rate_limited_function
:
make_rate_limited_function(function, delay) -> callable object
Bio.config._support.make_timed_function
:
make_timed_function(function, timeout[, retval2pickleable_fn][,
pickleable2retval_fn]) -> callable object
Bio.kNN.kNN
:
Holds information necessary to do nearest neighbors
classification.
Bio.pairwise2.affine_penalty
:
affine_penalty(open, extend[, penalize_extend_when_opening]) ->
gap_fn
Bio.pairwise2.dictionary_match
:
dictionary_match(score_dict[, symmetric]) -> match_fn
Bio.pairwise2.identity_match
:
identity_match([match][, mismatch]) -> match_fn
BioSQL.BioSeq.DBSeq
BioSQL.BioSeqDatabase.Adaptor
BioSQL.BioSeqDatabase.BioSeqDatabase
BioSQL.BioSeqDatabase.DBServer
BioSQL.DBUtils.Generic_dbutils
BioSQL.DBUtils.Mysql_dbutils
BioSQL.DBUtils.Pgdb_dbutils
:
Add support for pgdb in the PyGreSQL database connectivity
package.
BioSQL.DBUtils.Psycopg_dbutils
BioSQL.Loader.DatabaseLoader
:
Load a database with biopython objects.
BioSQL.Loader.DatabaseRemover
:
Complement the Loader functionality by fully removing a database.
Martel.Dispatch.DispatchHandler
Martel.Dispatch.Callback
Bio.StdHandler.Handle_dbid
Bio.StdHandler.Handle_dbxref
Bio.StdHandler.Handle_description
Bio.StdHandler.Handle_feature_location
Bio.StdHandler.Handle_feature_qualifier
Bio.StdHandler.Handle_features
Bio.StdHandler.Handle_hsp
Bio.StdHandler.Handle_hsp_seqalign
Bio.StdHandler.Handle_search_header
Bio.StdHandler.Handle_search_info
Bio.StdHandler.Handle_search_table
Bio.StdHandler.Handle_sequence
Martel.Dispatch.Dispatcher
:
Adapter from the standard SAX events
Bio.builders.Search.search.BuildSearch
Bio.builders.SeqRecord.sequence.BuildSeqRecord
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder
:
A SAX builder-style class to make a parsed SeqRecord available.
Bio.StdHandler.ConvertDispatchHandler
:
Used to read records and produce output through a Dispatcher
Martel.Dispatch.Multicall
Martel.Dispatch.RemapEnd
Martel.Dispatch.RemapStart
Martel.Expression.Expression
:
Base class for nodes in the Expression tree
Martel.Expression.Any
Martel.Expression.AnyEol
:
Match a newline (" ", " " or " ")
Martel.Expression.Assert
Martel.Expression.AtBeginning
:
Match the beginning of a line
Martel.Expression.AtEnd
:
Match the end of a line
Martel.Expression.Debug
Martel.Expression.Dot
:
Match any character except newline
Martel.Expression.ExpressionList
:
shares implementation used by 'Expressions with subexpressions'
Martel.Expression.Alt
:
An Expression tree with a list of alternate matches.
Martel.Expression.Seq
:
An Expression matching a set of subexpressions, in sequential
order
Martel.Expression.Group
Martel.Expression.GroupRef
Martel.Expression.Literal
Martel.Expression.MaxRepeat
Martel.Expression.NullOp
Martel.Expression.PassThrough
Martel.Expression.Str
Martel.Generate.CheckAssert
Martel.Generate.CheckAssertNot
Martel.Generate.CheckGroupRef
Martel.Generate.GeneratorState
Martel.Generate.HandleRepeatCount
Martel.Generate.SetGroupValue
Martel.Generate._call_call
Martel.Generate._call_calltag
Martel.Generate.print_debug
:
Print debug information
Martel.Generate.print_info
:
Print information after each expression match
Martel.IterParser.IterHeaderFooter
Martel.IterParser.IterRecords
Martel.Iterator.EventStream
Martel.Iterator.HeaderFooterEventStream
Martel.Iterator.Iterate
Martel.Iterator.Iterator
Martel.Iterator.IteratorHeaderFooter
Martel.Iterator.IteratorRecords
Martel.Iterator.RecordEventStream
Martel.Iterator.StoreEvents
Martel.LAX.ElementInfo
Martel.LAX._IsIn
Martel.RecordReader.RecordReader
Martel.RecordReader.CountLines
:
Read a specified (fixed) number of lines
Martel.RecordReader.EndsWith
Martel.RecordReader.Everything
:
Reads everything
Martel.RecordReader.Nothing
:
Reads nothing
Martel.RecordReader.StartsWith
Martel.RecordReader.Until
Martel.convert_re.GroupNames
Martel.msre_parse.Pattern
Martel.msre_parse.SubPattern
Martel.msre_parse.Tokenizer
Martel.test.support.Storage
__builtin__.object
:
The most base type
__builtin__.basestring
:
Type basestring cannot be instantiated; it is the base for str and
unicode.
Bio.EUtils.Datatypes.CheckLinkSet
:
Results from 'ncheck' and 'lcheck' searches
This is used to check if a set of records has neighbors
or links.
Bio.Wise.psw.ColumnUnit
Bio.EUtils.DBIdsClient.DBIdsLookup
:
Look up information about a DBIds
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet
:
Base class for dealing with a set of records, reference by
identifier
Bio.EUtils.DBIdsClient.PublicationDBIdsRecordSet
:
a set of publication records, referenced by database identifier
Bio.EUtils.DBIdsClient.SequenceDBIdsRecordSet
:
a set of sequence records, referenced by database identifier
Bio.EUtils.DBIdsClient.DBIdsRecord
:
A single record on the server
Bio.EUtils.DBIdsClient.PublicationDBIdsRecord
:
a single publication record, referenced by database identifier
Bio.EUtils.DBIdsClient.SequenceDBIdsRecord
:
a single sequence record, referenced by database identifier
BioSQL.BioSeq.DBSeqRecord
:
BioSQL equivalent of the biopython SeqRecord object.
__builtin__.dict
:
dict() -> new empty dictionary.
Bio.PropertyManager.CreateDict
Bio.EUtils.Config.DatabaseDict
:
map from name to DatabaseInfo for that database name
Bio.SubsMat.FreqTable.FreqTable
Bio.FSSP.FSSPAlignDict
Bio.FSSP.FSSPTools.FSSPMultAlign
Bio.FSSP.FSSPSumDict
Martel.LAX.LAX
Bio.InterPro.Record
Bio.Ndb.Record
Bio.UniGene.Record
Bio.SubsMat.SeqMat
:
A Generic sequence matrix class The key is a 2-tuple containing the
letter indices of the matrix.
Bio.Index._InMemoryIndex
:
This creates an in-memory index file.
Bio.Index._ShelveIndex
:
An index file wrapped around shelve.
Bio.EUtils.HistoryClient.HistoryLookup
:
Look up information about a search in history
Bio.EUtils.HistoryClient.BaseHistoryRecordSet
Bio.EUtils.HistoryClient.HistoryRecord
:
Get information about a single record in a history
Bio.EUtils.Datatypes.LinkSetDb
:
Used in eLink with cmd == neighbor
Attributes are:
dbto -- the links are TO this database name
linkname -- the name for this set (eg, "pubmed_protein")
links -- list of Links, one per matching record (includes score)
List order is the sames as the XML, which is ordered from
most likely to least.
__builtin__.list
:
list() -> new list list(sequence) -> new list initialized from
sequence's items
Bio.AlignAce.Motif.Motif
:
A class representing sequence motifs.
Bio.Nexus.Nexus.Nexus
Bio.Wise.dnal.Statistics
:
Calculate statistics from an ALB report
__builtin__.type
:
type(object) -> the object's type type(name, bases, dict) -> a
new type
exceptions.Exception
:
Common base class for all exceptions.
Bio.Wise.psw.AlignmentColumnFullException
Bio.CAPS.AlignmentHasDifferentLengthsError
Bio.SubsMat.BadMatrix
:
Exception raised when verifying a matrix
Bio.Nexus.Nodes.ChainException
Bio.Crystal.Error
Bio.Crystal.CrystalError
:
message - description of error
Martel.msre_constants.error
Bio.EUtils.Datatypes.EUtilsError
:
Base class for all EUtils-specific errors
Bio.EUtils.Datatypes.EUtilsSearchError
:
Used when the ESearch XML says there is an ERROR
Bio.Blast.NCBIStandalone.LowQualityBlastError
:
Error caused by running a low quality sequence through BLAST.
Bio.Nexus.Nexus.NexusError
Bio.Nexus.Nodes.NodeException
Bio.Blast.NCBIStandalone.ShortQueryBlastError
:
Error caused by running a short query sequence through BLAST.
exceptions.StandardError
:
Base class for all standard Python exceptions.
exceptions.TypeError
:
Inappropriate argument type.
exceptions.ValueError
:
Inappropriate argument value (of correct type).
Bio.EUtils.POM.ValidationError
:
ValidationError This exception is raised when an attempt is made to
construct an XML POM tree that would be invalid.
Bio.Data.CodonTable.TranslationError
Bio.Nexus.Trees.TreeError
xml.sax._exceptions.SAXException
:
Encapsulate an XML error or warning.
Martel.Parser.ParserException
:
used when a parse cannot be done
Martel.Parser.ParserPositionException
Martel.Parser.ParserRecordException
:
used by the RecordParser when it can't read a record
markupbase.ParserBase
:
Parser base class which provides some common support methods used by
the SGML/HTML and XHTML parsers.
sgmllib.SGMLParser
Bio.NetCatch.ExtractUrls
Bio.InterPro.InterProParser
:
Parses InterPro sequence data into a Record object.
Bio.SGMLExtractor.LocalParser
Bio.File.MyParser
Bio.Ndb.NdbParser
:
Parses Ndb sequence data into a Record object.
Bio.UniGene.UniGeneParser
Bio.Blast.NCBIWWW._FormParser
:
Parse a form in an HTML page.
reportlab.graphics.shapes._DrawTimeResizeable
:
Addin class to provide the horribleness of _drawTimeResize
reportlab.graphics.shapes.UserNode
:
A simple template for creating a new node.
reportlab.graphics.widgetbase.Widget
:
Base for all user-defined widgets.
Bio.Graphics.BasicChromosome._ChromosomeComponent
:
Base class specifying the interface for a component of the system.
Bio.Graphics.BasicChromosome.Chromosome
:
Class for drawing a chromosome of an organism.
Bio.Graphics.BasicChromosome.ChromosomeSegment
:
Draw a segment of a chromosome.
Bio.Graphics.BasicChromosome.TelomereSegment
:
A segment that is located at the end of a linear chromosome.
Bio.Graphics.BasicChromosome.Organism
:
Top level class for drawing chromosomes.
reportlab.graphics.widgetbase.PropHolder
:
Base for property holders
reportlab.graphics.widgetbase.Widget
:
Base for all user-defined widgets.
Bio.Graphics.BasicChromosome._ChromosomeComponent
:
Base class specifying the interface for a component of the system.
Bio.Graphics.BasicChromosome.Chromosome
:
Class for drawing a chromosome of an organism.
Bio.Graphics.BasicChromosome.ChromosomeSegment
:
Draw a segment of a chromosome.
Bio.Graphics.BasicChromosome.TelomereSegment
:
A segment that is located at the end of a linear chromosome.
Bio.Graphics.BasicChromosome.Organism
:
Top level class for drawing chromosomes.
xml.sax.handler.ContentHandler
:
Interface for receiving logical document content events.
Martel.test.test_macros.Capture
Martel.test.test_delimiter.CatchFields
Martel.test.support.CheckGood
Bio.StdHandler.ConvertHandler
:
Used to read records and produce output
Martel.test.test_Parser.CountRecords
Martel.Dispatch.Dispatcher
:
Adapter from the standard SAX events
Bio.builders.Search.search.BuildSearch
Bio.builders.SeqRecord.sequence.BuildSeqRecord
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder
:
A SAX builder-style class to make a parsed SeqRecord available.
Bio.StdHandler.ConvertDispatchHandler
:
Used to read records and produce output through a Dispatcher
Martel.test.support.Dump
Bio.ParserSupport.EventGenerator
:
Handler to generate events associated with a Martel parsed file.
Martel.test.test_optimize.GetErrorPos
Martel.test.test_attrs.GrabElements
Bio.Mindy.XPath.GrabXPathNodes
Martel.LAX.LAX
Bio.StdHandler.RecognizeHandler
Bio.Medline.NLMMedlineXML._IndexerHandler
:
Handles the results from the nlmmedline_format.
Bio.Blast.NCBIXML._XMLparser
:
Generic SAX Parser
Bio.Blast.NCBIXML.BlastParser
:
Parse XML BLAST data into a Record.Blast object
xml.sax.handler.ErrorHandler
:
Basic interface for SAX error handlers.
xml.sax.xmlreader.AttributesImpl
xml.sax.xmlreader.XMLReader
:
Interface for reading an XML document using callbacks.
Martel.Parser.HeaderFooterParser
:
Header followed by 0 or more records followed by a footer
Martel.Parser.Parser
:
Parse the input data all in memory
Martel.Parser.RecordParser
:
Parse the input data a record at a time
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