11/4/2013 BCHB524 - 2013 - Edwards

Advanced Python Concepts:

OOP & Inheritance

BCHB5242013

Lecture 18

11/4/2013 BCHB524 - 2013 - Edwards

Last time...

Object oriented programing (OOP) Enables us to describe, and program with,

concepts A class describes the behavior of the object

Data members (information storage) Methods (actions which manipulate the object)

Each instance of the class behaves as defined by the class. Typically each instance has different values in the

class’ internal data-members.2

11/4/2013 BCHB524 - 2013 - Edwards

Complete DNASeq.py Module

class DNASeq:    def __init__(self,seq="",name=""):        self.seq = seq        self.name = name    def read(self,filename):        self.seq = ''.join(open(filename).read().split())    def reverse(self):        return self.seq[::-1]    def complement(self):        d = {'A':'T','C':'G','G':'C','T':'A'}        return ''.join(map(d.get,self.seq))    def reverseComplement(self):        return ''.join(reversed(self.complement()))    def length(self):        return len(self.seq)    def freq(self,nuc):        return self.seq.count(nuc)    def percentGC(self):        gccount = self.freq('C') + self.freq('G')        return 100*float(gccount)/self.length()

3

Describe class in a module, then access using an import statement

11/4/2013 BCHB524 - 2013 - Edwards

Complete DNASeq.py Module

from DNAseq import DNAseq

ds = DNASeq('ACGTACGTACGTACGT','My sequence')print ds.complement(),ds.length(),ds.reverseComplement()print ds.freq('C'),ds.freq('G'),ds.length(),ds.percentGC()

ds = DNASeq()ds.read('anthrax_sasp.nuc')print ds.complement(),ds.length(),ds.reverseComplement()print ds.freq('C'),ds.freq('G'),ds.length(),ds.percentGC()

4

11/4/2013 BCHB524 - 2013 - Edwards

Class Inheritance

Inheritance allows similar classes or concepts to share common data and methods

Classic example: DNA Sequence, Transcript, Protein All contain a name and a sequence data-member All require length, is_valid methods Otherwise, specific differences in their details

5

11/4/2013 BCHB524 - 2013 - Edwards

Diagram Seq

seqname

length()freq()is_valid()

Protein

mw

valid_symbol()molWt()

DNA

comp

valid_symbol()reverseComplement()

Base-class“Parent”

Derived classes“Children”

6

11/4/2013 BCHB524 - 2013 - Edwards

Sequence objects: Sequence.py

class Seq:    def __init__(self,seq,name):        self.seq = seq        self.name = name    def length(self):        return len(self.seq)    def freq(self,sym):        return self.seq.count(sym)    def is_valid(self):        for sym in self.seq:            if not self.valid_symbol(sym):                return False        return True

class DNA(Seq):    comp = {'A':'T','C':'G','G':'C','T':'A'}    def valid_symbol(self,sym):        if sym in 'ACGT':            return True        return False    def reverseComplement(self):        return ''.join(map(self.comp.get,self.seq[::-1])) 7

11/4/2013 BCHB524 - 2013 - Edwards

Sequence objects: Sequence.py

class Seq:    def __init__(self,seq,name):        self.seq = seq        self.name = name    def length(self):        return len(self.seq)    def freq(self,sym):        return self.seq.count(sym)    def is_valid(self):        for sym in self.seq:            if not self.valid_symbol(sym):                return False        return Trueclass Protein(Seq):    mw = {'A': 71.04, 'C': 103.01, 'D': 115.03, 'E': 129.04, 'F': 147.07,          'G': 57.02, 'H': 137.06, 'I': 113.08, 'K': 128.09, 'L': 113.08,          'M': 131.04, 'N': 114.04, 'P': 97.05, 'Q': 128.06, 'R': 156.10,          'S': 87.03, 'T': 101.05, 'V': 99.07, 'W': 186.08, 'Y': 163.06 }    def valid_symbol(self,sym):        if sym in 'ACDEFGHIKLMNPQRSTVWY':            return True        return False    def molWt(self):        return sum(map(self.mw.get,self.seq))

8

11/4/2013 BCHB524 - 2013 - Edwards

Sequence objects

Using Sequence.py

from Sequence import *

s1 = DNA('ACGTACGTACGTACGT','DNA1')if s1.is_valid():    print s1.reverseComplement(), s1.length(), s1.freq('A')s2 = Protein('ACDEFGHIKL','Prot1')if s2.is_valid():    print s2.molWt(), s2.length(), s2.freq('H')

9

11/4/2013 BCHB524 - 2013 - Edwards

Diagram Seq

seqname

length()is_valid()

Protein

mw

valid_symbol()molWt()

DNA

comp

valid_symbol()reverseComplement()

Abstract base-class“Parent”

Derived classes“Children”

10

11/4/2013 BCHB524 - 2013 - Edwards

Base-class method using derived-class data member

class Seq:    def __init__(self,seq,name):        self.seq = seq        self.name = name    def length(self):        return len(self.seq)    def freq(self,sym):        return self.seq.count(sym)    def is_valid(self):        for sym in self.seq:            if sym not in self.valid_sym:                return False        return Trueclass DNA(Seq):    comp = {'A':'T','C':'G','G':'C','T':'A'}    valid_sym = 'ACGT'    def reverseComplement(self):        return ''.join(map(self.comp.get,self.seq[::-1]))class Protein(Seq):    mw = {'A': 71.04, 'C': 103.01, 'D': 115.03, 'E': 129.04, 'F': 147.07,          'G': 57.02, 'H': 137.06, 'I': 113.08, 'K': 128.09, 'L': 113.08,          'M': 131.04, 'N': 114.04, 'P': 97.05, 'Q': 128.06, 'R': 156.10,          'S': 87.03, 'T': 101.05, 'V': 99.07, 'W': 186.08, 'Y': 163.06 }    valid_sym = 'ACDEFGHIKLMNPQRSTVWY'    def molWt(self):        return sum(map(self.mw.get,self.seq))

11

11/4/2013 BCHB524 - 2013 - Edwards

Revisit the CodonTable module

class CodonTable:    data = None

    def __init__(self,filename=None):        if filename:            data = open(filename).read()            self.parse(data)        else:            self.parse(self.data)

    def parse(self,data):        lines = {}        for l in data.split('\n'):            sl = l.split()            try:                key = sl[0]                value = sl[2]                lines[key] = value            except IndexError:                pass

        b1 = lines['Base1']        b2 = lines['Base2']        b3 = lines['Base3']        aa = lines['AAs']        st = lines['Starts']

        self.table = {}        n = len(aa)        for i in range(n):            codon = b1[i] + b2[i] + b3[i]            isInit = (st[i] == 'M')            self.table[codon] = (aa[i],isInit)        return

    def aa(self,codon):        try:            return self.table[codon][0]        except KeyError:            return 'X'

    def translate(self,seq,frame):        aaseq = []        for codon in seq.codons(frame):            aaseq.append(self.aa(codon))        return ''.join(aaseq)

12

11/4/2013 BCHB524 - 2013 - Edwards

Revisit the CodonTable module

class CodonTable:    data = None    def __init__(self,filename=None):        if filename:            data = open(filename).read()            self.parse(data)        else:            self.parse(self.data) # ...

class StandardCode(CodonTable):    data = """  AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGStarts = ---M---------------M---------------M----------------------------Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGBase2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGBase3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG"""

class BacterialCode(CodonTable):    data = """  AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGGStarts = ---M---------------M------------MMMM---------------M------------Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGGBase2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGBase3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG""" 13

11/4/2013 BCHB524 - 2013 - Edwards

Add codons to the DNA classclass Seq:    def __init__(self,seq,name):        self.seq = seq        self.name = name    def length(self):        return len(self.seq)    def freq(self,sym):        return self.seq.count(sym)    def is_valid(self):        for sym in self.seq:            if sym not in self.valid_sym:                return False        return Trueclass DNA(Seq):    comp = {'A':'T','C':'G','G':'C','T':'A'}    valid_sym = 'ACGT'    def reverseComplement(self):        return ''.join(map(self.comp.get,self.seq[::-1]))    def codons(self,frame):        result = []        for i in range(frame-1,len(self.seq),3):            result.append(self.seq[i:i+3])        return result

14

from Sequence import *from CodonTable import *

s1 = DNA('ACGTACGTACGTACGT','DNA1')ct = StandardCode()

print ct.translate(s1,2)

11/4/2013 BCHB524 - 2013 - Edwards

Using the CodonTable module

15