1. Advanced Python Concepts: Object Oriented Programming
BCHB524 Lecture 17
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2. Using Classes
We've actually been using objects and their methods already!
s = 'ACGTACGTACGTACGT' print s.count('T') print s.replace('T','U') l = [6,5,4,3,2,1] l.append(10) l.sort() s = set() s.add(1) s.add(2)
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3. Using Classes
We've actually been using objects and their methods already!
import Bio.SeqIO thefile = open("ls_orchid.fasta") for seq_record in Bio.SeqIO.parse(thefile, "fasta"):     print seq_record.id     print seq_record.description     print seq_record.seq thefile.close()
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4. Using Classes Classes make instances of objects
string is a class, 'ACGT' is an instance of a string.
Make new instances using class name:
s = string(), d = dict(), s = set(), i = int(2)
Objects can hold information
seq_record.id, seq_record.seq, seq_record.annotations
Called data members or attributes
Objects can perform actions
s = 'ACGT'; print s.count('a')
Called methods
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5. Classes as Concepts
Classes allow us to add new concepts to a language.
Suppose we wanted to add a "DNA sequence" concept to python
What information should "DNA sequence" capture?
What actions or operations should "DNA sequence" provide?
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6. DNA Sequence Class Data members: Methods: sequence, name, organism.
length, reverse, complement, reverseComplement, transcribe, translate percentGC, initMet, freq
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7. DNA Sequence Class
class DNASeq:     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) ds = DNASeq() ds.seq = 'ACGTACGTACGT' ds.name = 'My sequence' print ds.complement(),ds.length(),ds.reverseComplement()
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8. DNA Sequence Class
class DNASeq:     #....     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() ds = DNASeq() ds.seq = 'ACGTACGTACGT' ds.name = 'My sequence' print ds.freq('C'),ds.freq('G'),ds.length(),ds.percentGC()
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9. DNA Sequence Class
The special method __init__ is called when a new instance is created.
Used to initialize data-members.
Forces class user to provide valid initial information.
class DNASeq:     def __init__(self,seq,name):         self.seq = seq         self.name = name     #.... ds = DNASeq('ACGTACGTACGTACGT', 'My sequence') print ds.freq('C'),ds.freq('G'),ds.length(),ds.percentGC()
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10. DNA Sequence Class
Somtimes __init__ is used to set up an "empty" instance.
Other methods or data-members used to instantiate
class DNASeq:     def __init__(self):         self.seq = ""         self.name = ""     def read(self,filename):         self.seq = ''.join(open(filename).read().split()) #.... ds = DNASeq() ds.name = 'Anthrax SASP' ds.read('anthrax_sasp.nuc') print ds.freq('C'),ds.freq('G'),ds.length(),ds.percentGC()
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11. DNA Sequence Class
Default arguments allow us to set up "empty", partial, or completely instantiated instances.
class DNASeq:     def __init__(self,seq="",name=""):         self.seq = seq         self.name = name     def read(self,filename):         self.seq = ''.join(open(filename).read().split())     #.... ds = DNASeq(name='Anthrax SASP') ds.read('anthrax_sasp.nuc') print ds.freq('C'),ds.freq('G'),ds.length(),ds.percentGC()
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12. 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()
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13. 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()
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14. A class for codon tables
Method calls, for instance "codons":
codons.read(filename)
stores the contents of filename in the codon_table object.
codons.amino_acid(codon)
returns amino-acid symbol for codon
codons.is_init(codon)
returns true if codon is an initiation codon false, otherwise
codons.get_ambig_aa (codon)
returns single amino-acid represented by a codon with N's
codons.startswith_init(seq)
returns true if DNA sequence seq starts with init codon
codons.translate(seq,frame)
returns amino-acid sequence for DNA sequence seq
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15. A class for codons
from DNASeq import * from codon_table import * import sys if len(sys.argv) < 3:     print "Require codon table and DNA sequence on command-line."     sys.exit(1) codons = codon_table() codons.read(sys.argv[1]) seq = DNASeq() seq.read(sys.argv[2]) if codons.startswith_init(seq):     print "Initial codon is an initiation codon" for frame in (1,2,3):     print "Frame",frame,"(forward):",codons.translate(seq,frame)
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16. A class for codons In codon_table.py:
class codon_table:     def __init__(self):         self.table = {}     def read(self,filename):         # magic     def amino_acid(self,codon):         # magic         return aa     def is_init(self,codon):         # magic         return result     def get_ambig_aa(self,codon):         # magic         return aa     def startswith_init(self,seq):         # magic         return result
def translate(self,seq,frame):         # magic         return aaseq
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17. Side by side
from DNASeq import * from codon_table import * import sys if len(sys.argv) < 3:     print "Require codon table and", \           "DNA sequence on command-line."     sys.exit(1) codons = codon_table() codons.read(sys.argv[1]) seq = DNASeq() seq.read(sys.argv[2]) if codons.startswith_init(seq):     print "Initial codon" print codons.translate(seq,1)
from MyNucStuff import * from codon_table import * import sys if len(sys.argv) < 3:     print "Require codon table and", \           "DNA sequence on command-line."     sys.exit(1)
codons = read_codons(sys.argv[1]) seq = read_seq(sys.argv[2]) if is_init(codons,seq[:3]):     print "Initial codon" print translate(codons,seq,1)
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18. Exercise
Convert your modules for DNA sequence and codons to a codon_table and DNASeq class.
Demonstrate the use of this module and the codon table module to translate an amino-acid sequence in all six-frames with just a few lines of code.
Hint: just import the new classes from their module(s) and call the necessary methods/functions!
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19. Homework 8 Due Monday, November 6th. Exercise from Lecture 16
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