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Python Programming for Biology
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Python Programming for Biology_ - Tim J. Stevens
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PythonProgrammingforBiology
BioinformaticsandBeyond
Do you have a biological question that could be readily answered by computational
techniques,butlittleexperienceinprogramming?Do you want to learn more about the
core techniques used in computational biology and bioinformatics? Written in an
accessible style, this guide provides a foundation for both newcomers to computer
programming and those who want to learn more about computational biology. The
chapters guide the reader through: a complete beginners’ course to programming in
Python, with an introduction to computing jargon; descriptions of core bioinformatics
methodswithworkingPythonexamples;scientificcomputingtechniques,includingimage
analysis,statisticsandmachinelearning.Thisbookalsofunctionsasalanguagereference
writteninstraightforwardEnglish,coveringthemostcommonPythonlanguageelements
and a glossary of computing and biological terms. This title will teach undergraduates,
postgraduatesandprofessionalsworkinginthelifescienceshowtoprogramwithPython,
apowerful,flexibleandeasy-to-uselanguage.
TIMJ.STEVENS,abiochemistbytraining,isaSeniorInvestigatorScientistattheMRC
LaboratoryofMolecularBiologyinCambridge.Heresearchesthree-dimensionalgenome
architecture and provides computational biology oversight, development and training
withintheCellBiologyDivision.
WAYNEBOUCHER,a mathematician and theoretical physicist by training, is a Senior
Post-DoctoralAssociateandcomputingtechnicianfortheDepartmentofBiochemistryat
the University of Cambridge. He teaches undergraduate mathematics and postgraduate
programming courses. Wayne is currently developing software for the analysis of
biologicalmoleculesbynuclearmagneticresonancespectroscopy.
PythonProgrammingforBiology
BioinformaticsandBeyond
TimJ.Stevens
MRCLaboratoryofMolecularBiology
and
WayneBoucher
UniversityofCambridge
UniversityPrintingHouse,CambridgeCB28BS,UnitedKingdom
CambridgeUniversityPressispartoftheUniversityofCambridge.
ItfurtherstheUniversity’smissionbydisseminatingknowledgeinthepursuitof
education,learningandresearchatthehighestinternationallevelsofexcellence.
www.cambridge.org
Informationonthistitle:www.cambridge.org/9780521895835
©TimJ.StevensandWayneBoucher,2015
Thispublicationisincopyright.Subjecttostatutoryexceptionandtotheprovisionsof
relevantcollectivelicensingagreements,noreproductionofanypartmaytakeplace
withoutthewrittenpermissionofCambridgeUniversityPress.
Firstpublished2015
PrintedintheUnitedKingdombyTJInternationalLtd,PadstowCornwall
AcataloguerecordforthispublicationisavailablefromtheBritishLibrary
LibraryofCongressCataloguinginPublicationdata
Stevens,TimJ.,1976–
Pythonprogrammingforbiology,bioinformatics,andbeyond/TimJ.Stevens,University
ofCambridge,Wayne
Boucher,UniversityofCambridge.
pagescm
Includesindex.
ISBN978-0-521-89583-5(Hardback)–ISBN978-0-521-72009-0(Paperback)
1.Biology–Dataprocessing.2.Python(Computerprogramlanguage)I.Boucher,Wayne.
II.Title.
QH324.2.S7272014
570.285–dc232014021017
ISBN978-0-521-89583-5Hardback
ISBN978-0-521-72009-0Paperback
Additionalresourcesforthispublicationatwww.cambridge.org/pythonforbiology
CambridgeUniversityPresshasnoresponsibilityforthepersistenceoraccuracyofURLs
forexternalorthird-partyinternetwebsitesreferredtointhispublication,anddoesnot
guaranteethatanycontentonsuchwebsitesis,orwillremain,accurateorappropriate.
Contents
Preface
Acknowledgements
1 Prologue
Pythonprogrammingforbiology
2 Abeginners’guide
Programmingprinciples
Basicdatatypes
Programflow
3 Pythonbasics
Introducingthefundamentals
Simpledatatypes
Collectiondatatypes
Importingmodules
4 Programcontrolandlogic
Controllingcommandexecution
Conditionalexecution
Loops
Errorexceptions
Furtherconsiderations
5 Functions
Functionbasics
Inputarguments
Variablescope
Furtherconsiderations
6 Files
Computerfiles
Readingfiles
Filereadingexamples
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