【生物信息学编程使用Python】BPUP

BioinformaticsProgrammingUsingPythonBioinformaticsProgrammingUsingPythonMitchellLModelBeijing•Cambridge•Farnham•Köln•Sebastopol•Taipei•TokyoBioinformaticsProgrammingUsingPythonbyMitchellLModelCopyright©2010MitchellLModel.Allrightsreserved.PrintedintheUnitedStatesofAmerica.PublishedbyO’ReillyMedia,Inc.,1005GravensteinHighwayNorth,Sebastopol,CA95472.O’Reillybooksmaybepurchasedforeducational,business,orsalespromotionaluse.Onlineeditionsarealsoavailableformosttitles().Formoreinformation,contactourcorporate/institutionalsalesdepartment:[e-mail]:MikeLoukidesProductionEditor:SarahSchneiderCopyeditor:RachelHeadProofreader:SadaPreischIndexer:LucieHaskinsCoverDesigner:KarenMontgomeryInteriorDesigner:DavidFutatoIllustrator:RobertRomanoPrintingHistory:December2009:FirstEdition.O’ReillyandtheO’ReillylogoareregisteredtrademarksofO’ReillyMedia,Inc.BioinformaticsPro-grammingUsingPython,theimageofabrownrat,andrelatedtradedressaretrademarksofO’ReillyMedia,Inc.Manyofthedesignationsusedbymanufacturersandsellerstodistinguishtheirproductsareclaimedastrademarks.Wherethosedesignationsappearinthisbook,andO’ReillyMedia,Inc.wasawareofatrademarkclaim,thedesignationshavebeenprintedincapsorinitialcaps.Whileeveryprecautionhasbeentakeninthepreparationofthisbook,thepublisherandauthorassumenoresponsibilityforerrorsoromissions,orfordamagesresultingfromtheuseoftheinformationcon-tainedherein.TMThisbookusesRepKover,adurableandflexiblelay-flatbinding.ISBN:978-0-596-15450-9[M]1259959883TableofContentsPreface.....................................................................xi1.Primitives.............................................................1SimpleValues1Booleans2Integers2Floats3Strings4Expressions5NumericOperators5LogicalOperations7StringOperations9Calls12CompoundExpressions16Tips,Traps,andTracebacks18Tips18Traps20Tracebacks202.Names,Functions,andModules..........................................21AssigningNames23DefiningFunctions24FunctionParameters27CommentsandDocumentation28Assertions30DefaultParameterValues32UsingModules34Importing34PythonFiles38Tips,Traps,andTracebacks40Tips40vTraps45Tracebacks463.Collections............................................................47Sets48Sequences51Strings,Bytes,andBytearrays53Ranges60Tuples61Lists62Mappings66Dictionaries67Streams72Files73Generators78Collection-RelatedExpressionFeatures79Comprehensions79FunctionalParameters89Tips,Traps,andTracebacks94Tips94Traps96Tracebacks974.ControlStatements....................................................99Conditionals101Loops104SimpleLoopExamples105InitializationofLoopValues106LoopingForever107LoopswithGuardConditions109Iterations111IterationStatements111KindsofIterations113ExceptionHandlers134PythonErrors136ExceptionHandlingStatements138RaisingExceptions141ExtendedExamples143ExtractingInformationfromanHTMLFile143TheGrandUnifiedBioinformaticsFileParser146ParsingGenBankFiles148TranslatingRNASequences151ConstructingaTablefromaTextFile155vi|TableofContentsTips,Traps,andTracebacks160Tips160Traps162Tracebacks1635.Classes..............................................................165DefiningClasses166InstanceAttributes168ClassAttributes179ClassandMethodRelationships186Decomposition186Inheritance194Tips,Traps,andTracebacks205Tips205Traps207Tracebacks2086.Utilities.............................................................209SystemEnvironment209DatesandTimes:datetime209SystemInformation212Command-LineUtilities217Communications223TheFilesystem226OperatingSystemInterface:os226ManipulatingPaths:os.path229FilenameExpansion:fnmatchandglob232ShellUtilities:shutil234ComparingFilesandDirectories235WorkingwithText238FormattingBlocksofText:textwrap238StringUtilities:string240Comma-andTab-SeparatedFormats:csv241String-BasedReadingandWriting:io242PersistentStorage243PersistentText:dbm243PersistentObjects:pickle247KeyedPersistentObjectStorage:shelve248DebuggingTools249Tips,Traps,andTracebacks253Tips253Traps254Tracebacks255TableofContents|vii7.PatternMatching.....................................................257FundamentalSyntax258Fixed-LengthMatching259Variable-LengthMatching262GreedyVersusNongreedyMatching263GroupingandDisjunction264TheActionsofthereModule265Functions265Flags266Methods268ResultsofreFunctionsandMethods269MatchObjectFields269MatchObjectMethods269PuttingItAllTogether:Examples270SomeQuickExamples270ExtractingDescriptionsfromSequenceFiles272ExtractingEntriesFromSequenceFiles274Tips,Traps,andTracebacks283Tips283Traps284Tracebacks2858.StructuredText.......................................................287HTML287SimpleHTMLProcessing289StructuredHTMLProcessing297XML300TheNatureofXML300AnXMLFileforaCompleteGenome302TheElementTreeModule303Event-BasedProcessing310expat317Tips,Traps,andTracebacks322Tips322Traps323Tracebacks3239.WebProgramming....................................................325ManipulatingURLs:urllib.parse325DisassemblingURLs326AssemblingURLs327OpeningWebPages:webbrowser328ModuleFu