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ProgramminginPython

MichaelSchroederSebas0anSalen0n

UpdatesbyAndreasHenschel

Lecture1:Datatypes,Condi0ons,andLoops

SlidesderivedfromIanHolmes,DepartmentofSta0s0cs,UniversityofOxford

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Objec0vesofthiscourse

•  Conceptsofcomputerprogramming•  RudimentaryPython(widely-usedlanguage)

•  Introduc0ontoBioinforma0csfileformats

•  Prac0caldata-handlingalgorithms

•  Exposuretobioinforma0cslibraries

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Mo0va0on

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AllthesesequencesarewingedhelixDNAbindingdomains. Howcanwegroupthemintofamilies?

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Mo0va0onLet'srebuildSCOPfamilies!

•  GivenaSCOPsuperfamilyanditssequences ->howcanwedivideitintofamilies?

•  First,weneeddynamicprogrammingtodeterminethesequencesimilarity

•  Thenwedothefollowing:– Forallpairsofsequences,callthesequencesimilarityalgorithmandrecordthesimilarityintoadistancematrix

– Next,runhierarchicalclusteringtoclusterthesequences.

Whichprogrammingstepsarenecessary?

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WhyPython?

•  WellsuitedforscripFng,easysyntax•  capableofobject-orientedprogramming•  Complexdatatypesandlargeprojectsfeasible•  Availabilityandreuseofcode(e.g.BioPython)•  Universallanguage,applica0onsinandbeyondbioinforma0cs:Galaxy,PyMOL,Tophat,etc.

•  Compa0blewithmostso]waretechnologies:GUI,MPI,OpenGL,RDB

•  TestcomplicatedexpressionsinthePythonshell

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Styleofthislecture

•  Thecolorschemeforprograms,outputandtextfiles:

•  Interac0onwiththePythonshell:veryhandyforquicktests.Helpsbeginnerstoovercomephysiologicalbarrier:Goahead,trythingsout!

The main program The program output Files are shown in yellow

Thefilenamegoeshere

>>> (Python Expression) (immediate Python result)

Prompt,(pythonexpectsinputhere) PressEnter

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Generalprinciplesofprogramming

•  Makeincrementalchanges

•  Testeverythingyoudo–  usethePythonshellfortes0ngexpressions/func0ons

interac0vely–  theedit-run-revisecycle

•  Writesothatotherscanreadit–  (whenpossible,writewithothers)–  Documentcode

•  Thinkbeforeyouwrite•  Useagoodtexteditor/IDE

– vim,emacs,Atom–  (iPythonnotebooks)

YoucanusegeditonthePCPoolWorksta0ons

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Datatypes

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Pythonbasics

•  BasicsyntaxofaPythonprogram:

# Elementary Python program print "Hello World"

printstatementtellsPythontoprintthefollowingstufftothescreen

Singleordoublequotesenclosea"stringliteral"

Linesbeginningwith"#"arecomments,andareignoredbyPython

Hello World

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Variables

•  WecantellPythonto"remember"apar0cularvalue,usingtheassignmentoperator"=":

•  Thexisreferredtoasa"scalarvariable".Variablenamescancontainalphabe0ccharacters,numbers(butnotatthestartofthename),andunderscoresymbols"_"

x = 3 print x

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x = "ACGCGT" print x

ACGCGT

Bindingsiteforyeasttranscrip0onfactorMCB

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VariablesandObjects

•  EverythinginPythonisanobject•  Anobjectmodelsareal-worlden0ty•  objectspossessmethods(alsocalledfunc0ons)thataretypicallyappliedtotheobject,possiblyparameterized

•  objectscanalsopossessvariables,thatdescribetheirstate

•  e.g.x.upper()isaparameter-lessmethod,thatworksonthestringobjectx

Object . Methodorvariable

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Built-indatatypesandopera0onsI/II

•  TruthValuesandBoolean– None,True,False(arespecialtypeofintegers)– BooleanOpera0ons:and,or,not

•  Comparisons–  <,==,!=,isnot,…

•  Numerictypes–  Integersandfloa0ngpointnumbers– Arithme0copera0ons:x+y,x/y,abs(x),x**y,…

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Built-indatatypesandopera0onsII/II

•  Sequencetypes–  Strings,lists,tuples,…–  Opera0ons:concaten*on(+),len(x),xins,…–  Stringswithaddi0onalmethods:

•  capitalize,endswith,find,islower,lstrip,…

•  Settypes–  set,frozenset(can’tbechanged:immutable)

–  Opera0ons:len(s),issubset(other),union(s1,s2),add,…

•  MappingTypes–  dict:mapshashablekeystovalues–  Opera0ons:deld[key],keyind,…

• …andsomemore

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Arithme0copera0ons…

•  Basicoperatorsare+ - / * %x = 14 y = 3 print "Sum: ", x + y print "Product: ", x * y print "Remainder: ", x % y

Sum: 17 Product: 42 Remainder: 2

x = 5 print "x started as", x x = x * 2 print "Then x was", x x = x + 1 print "Finally x was" ,x

x started as 5 Then x was 10 Finally x was 11

Couldwritex *= 2 Couldwritex += 1

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…Orinterac0vely

>>> x = 14 >>> y = 3 >>> x + y 17 >>> x * y 42 >>> x % y 2 >>> x = 5 >>> print "x started as", x x started as 5 >>> x *= 2 >>> print "Then x was", x Then x was 10 >>> x += 1 >>> print "Finally x was", x Finally x was 11 >>>

• Thisway,youcanusePythonasacalculator

• Canalsouse+= -= /= *=

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Stringopera0ons

•  Concatena0on+ +=

•  Canfindthelengthofastringusingthefunc0onlen(x)

a = "pan" b = "cake" a = a + b print a

pancake

a = "soap" b = "dish" a += b print a

soapdish

mcb = "ACGCGT" print "Length of %s is "%mcb, len(mcb)

Length of ACGCGT is 6

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Stringformavng

•  Stringscanbeformawedwithplaceholdersforinsertedstrings(%s)andnumbers(%dfordigitsand%fforfloats)

•  UseOperator%onstrings:

>>> "aaaa%saaaa%saaa"%("gcgcgc","tttt") 'aaaagcgcgcaaaattttaaa' >>> "A range written like this: (%d - %d)" % (2,5) 'A range written like this: (2 - 5)' >>> "Or with preceeding 0's: (%03d - %04d)" % (2,5) "Or with preceeding 0's: (002 - 0005)" >>> "Rounding floats %.3f" % math.pi 'Rounding floats 3.142' >>> ”Scientific notation: %.3e" % 0.0000002345) ’Scientific notation: 2.345e-07'

FormawedString % Inser0onTuple

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Morestringopera0ons

x = "A simple sentence" print x print x.upper() print x.lower() xl=list(x) xl.reverse() print "".join(xl) x = x.replace("i", "a") print x print len(x)

A simple sentence A SIMPLE SENTENCE a simple sentence ecnetnes elpmis A A sample sentence 17

Converttouppercase

Converttolowercase

Convertthestringtoalist

Translate"i"'sinto"a"'s

Calculatethelengthofthestring

ReversethelistJoinalllistmembers

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Concatena0ngDNAfragments

dna1 = "accacgt" dna2 = "taggtct" print dna1 + dna2

"Transcribing"DNAtoRNA

accacguuaggucu

dna = "accACgttAGGTct" rna = dna.lower().replace("t", "u") print rna

Makeitalllowercase

DNAstringisamixtureofupper&lowercase

Replace"t"with"u"

accacgttaggtct

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Searchinginstrings

rna = ”accacguuaggucu” pattern = “cguu” Print rna.find(pattern)

4 accacguuaggucu012345678…

rna = ”accacguuaggucu” result = rna.endswith(“gg”) print result

False

rna = ”accacguuaggucu” print “cguu” in rna True

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CondiFons

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Condi0onalblocks

•  Theabilitytoexecuteanac*oncon0ngentonsomecondi*oniswhatdis0nguishesacomputerfromacalculator.InPython,thislookslikethis:

x = 149 y = 100 if x > y: print x,"is greater than",y else: print x,"is less than", y

149 is greater than 100

Theseindenta0ons tellPythonwhichpieceofcodeiscon0ngentonthecondi0on.

if condition: action else: alternative

Consistent,level-wiseinden0ngimportant

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Condi0onaloperators

•  Numeric:> >= < <= != ==

•  Thesameoperatorsworkonstringsasalphabe0ccomparisons

x = 5 * 4 y = 17 + 3 if x == y: print x, "equals", y 20 equals 20

Notethatthetestfor"xequalsy"isx==y,notx=y

(x, y) = ("Apple", "Banana") if y > x: print y, "after", x Banana after Apple

"doesnotequal"

Shorthandsyntaxforassigningmorethanonevariableata0me

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Logicaloperators•  Logicaloperators: and andor

•  Thekeywordnotisusedtonegatewhatfollows.Thusnot x < ymeansthesameasx >= y

•  ThekeywordFalse(orthevaluezero)isusedtorepresentfalsehood,whileTrue (oranynon-zerovalue,e.g.1)representstruth.Thus:

if True: print "True is true" if False: print "False is true" if -99: print "-99 is true"

True is true -99 is true

x = 222 if x % 2 == 0 and x % 3 == 0: print x, "is an even multiple of 3"

222 is an even multiple of 3

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Loops

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x = 0 while x < 10: print x, x+=1

0 1 2 3 4 5 6 7 8 9

Theindentedcodeisrepeatedlyexecutedaslongasthecondi0onx<10remainstrue

Loops

•  Here'showtoprintoutthenumbers0to9:

•  Thisisawhileloop.Thecodeisexecutedwhilethecondi0onistrue.

Equivalenttox = x + 1

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Acommonkindofloop

•  Let'sdissectthecodeofthewhileloopagain:

•  Alterna0vely,theforloopconstructiteratesthroughasequence(e.g.list,tuple,string)

x = 0 while x < 10: print x, x+=1

Ini0alisa0on

Testforcomple0on

Con0nua0on

for x in range(10): print x,

Itera0onvariable Generatesalist[0,1,…,9]

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Forloopfeatures•  Loopscanbeusedwithalliteratabletypes,ie.:lists,strings,tuples,iterators,sets,filehandlers

•  Stepsizescanbespecifiedwiththe3.argumentofthesliceconstructor(nega0vevaluesforitera0ngbackwards)

>>> for nucleotide in "actgc": ... print nucleotide, a c t g c

>>> for number in range(0,50,7) : ... print number, 0 7 14 21 28 35 42 49 >>> for nucleotide in "actgc"[::-1]: ... print nucleotide, c g t c a >>> print “HtaEdsLfgLdfOf”[::3] HELLO

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Enumerate•  Enumerateisahandymethodtotracktheindexwhenloopingoverasequence

•  Insteadof…

•  Wecanletdoenumeratedotheworkforus…

>>> i = 0 >>> for nuc in "actgc”: ... print “%i: %s” % (i+1, nuc) ... i +=1

>>> for i, nuc in enumerate("actgc”): ... print “%i: %s” % (i+1, nuc)

1: a 2: c 3: t 4: g 5: c

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ReadingDatafromFiles

•  Toreadfromafile,wecanconvenientlyiteratethroughitlinewisewithafor-loopandtheopenfunc0on.–  Internallyafilehandleismaintainedduringtheloop.

Thiscodesnippetopensafilecalled"sequence.txt"intheinthecurrentdirectory,anditeratesthroughitlinebyline

for line in open("sequence.txt"): print line,

>CG11604 TAGTTATAGCGTGAGTTAGT TGTAAAGGAACGTGAAAGAT AAATACATTTTCAATACC

>CG11604 TAGTTATAGCGTGAGTTAGT TGTAAAGGAACGTGAAAGAT AAATACATTTTCAATACC

sequence.txt

Thecommapreventsprint'sautoma0cnewline

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Howto…

•  sumupallthenumbersin[3,7,10,4,-1,0]?

•  printallwordin[‘Oranges’,‘Bananas’,‘Cucumbers’,‘Apples’]star0ngwithanOorA?

•  checkwhichelementof[1,5,-1,8,7]arealsoinside[8,7,10,5,0,0]?

•  checkifthera0ooftwointegersaandbislargerthan0.5?

•  checkforalltuplesin[(3,2),(10,5),(1,-1)]ifthesquareofthefirstnumbercanbedividedbythesecondwithoutrest?

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Summary

•  EverythinginPythonisanobject•  Built-indatatypes:numeric,sequences,sets,mappings

•  Controlstructures:LoopsandCondi0ons– Forloop&whileloop– if,else,elif,<,>,==,!=,etc.

•  PythonwellsuitedforstringmanipulaFon– Lotsofstring-specificmethods