1. Advanced Python Concepts: OOP & Inheritance
BCHB524 Lecture 18
BCHB524 - Edwards

2. 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.
BCHB524 - Edwards

3. 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()
BCHB524 - Edwards

4. Complete DNASeq.py Module
Describe class in a module, then access using an import statement
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()
BCHB524 - Edwards

5. 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
BCHB524 - Edwards

6. Diagram Seq DNA Protein seq name length() freq() is_valid() Base-class
“Parent”
DNA
comp
valid_symbol()
reverseComplement()
Protein mw
valid_symbol()
molWt()
Derived classes
“Children”
BCHB524 - Edwards

7. 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]))
BCHB524 - Edwards

8. 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 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))
BCHB524 - Edwards

9. 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')
BCHB524 - Edwards

10. Diagram Seq DNA Protein seq name length() is_valid()
Abstract base-class
“Parent”
DNA
comp
valid_symbol()
reverseComplement()
Protein mw
valid_symbol()
molWt()
Derived classes
“Children”
BCHB524 - Edwards

11. 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 True class 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))
BCHB524 - Edwards

12. 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)
BCHB524 - Edwards

13. 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*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts = ---M M M Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG """ class BacterialCode(CodonTable):     data = """   AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts = ---M M MMMM M Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG """
BCHB524 - Edwards

14. Add codons to the DNA class
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 True class 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
BCHB524 - Edwards

15. Using the CodonTable module
from Sequence import * from CodonTable import * s1 = DNA('ACGTACGTACGTACGT','DNA1') ct = StandardCode() print ct.translate(s1,2)
BCHB524 - Edwards