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

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

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

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

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

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

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

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

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

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

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

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

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