1. Advanced Python Data Structures
BCHB524 Lecture 7
BCHB524 - Edwards

2. Outline Review of list data-structures Advanced Data-structures
Dictionaries, Sets, Files
Reading, parsing files (codon tables)
Exercises
BCHB524 - Edwards

3. Data-structures: Lists
Compound data-structure:
Many objects in order numbered from 0
[] indicates list.
Item access and iteration
Same as for string, "l[i]" for item i
"for item in l" for each item of the list.
List modification
items can be changed, added, or deleted.
Range is a list
String ↔ List
BCHB524 - Edwards

4. Python Data-structures: Dictionaries
Compound data-structure, stores any number of arbitrary key-value pairs.
Keys and/or value can be different types
Can be empty
Values can be accessed by key
Keys, values, or pairs can be accessed by iteration
Values can be changed
Key, value pairs can be added
Key, value pairs can be deleted
BCHB524 - Edwards

5. Dictionaries: Syntax and item access
# Simple dictionary d = {'a': 1, 'b': 2, 'acdef': 3} print d # Access value using its key print d['a'] # Change value associated with a key d['acdef'] = 5 print d # Add value by assigning to a dictionary key d['newkey'] = 10 print d
BCHB524 - Edwards

6. Dictionaries: Iteration
# Initialize d = {'a': 1, 'b': 2, 'acdef': 5, 'newkey': 10} # keys from d print d.keys() # values from d print d.values() # key-value pairs from d print d.items() # Iterate through the keys of d for k in d.keys():     print k, print # Iterate through the key-value pairs of d for k,v in d.items():     print k,"=",v, print
BCHB524 - Edwards

7. Dictionaries: Different from lists?
# Initialize d = {} # Add some values, integer keys! d[0] = 1 d[1] = 2 d[10] = 1000 # See how the dictionary looks print d # Test whether a key is in the dictionary print "Is key 15 in d?",d.has_key(15) # Access value with key 15 with default -1 print "Value for key 15, or -1:",d.get(15,-1) # Access value with key 15 - error! print "Value for key 15:",d[15]
d = {}
d[0] = 1
d[1] = 2
d[10] = 1000
print d
d.has_key(15)
d.get(15,-1)
BCHB524 - Edwards

8. Python Data-structures: Sets
Compound data-structure, stores any number of arbitrary distinct data-items.
Data-items can be different types
Can be empty
Items can be accessed by iteration only.
Items can be tested for membership.
Items can be added
Items can be deleted
BCHB524 - Edwards

9. Sets: Add and Test Elements
# Make an empty set s = set() print s # Add an element, and then a list of elements s.add('a') s.update(['b','c','d']) print s # Test for membership print "e is in s",('e' in s) print "e is not in s",('e' not in s) print "c is in s",('c' in s)
s = set() s
s.add('a')
s.update(['b','c','d'])
'e' in s
False
'e' not in s
True
'c' in s
BCHB524 - Edwards

10. Python Data-structures: Files
Read strings from file, or
Write strings to file.
Get access to lines as strings by iteration.
…or get the entire contents of the file as a string
Write by printing strings to file.
MUST open and close files:
Need to indicate whether we want to read or write.
BCHB524 - Edwards

11. Files: Reading
# Open a file, store "handle" in f f = open('anthrax_sasp.nuc') # MAGIC! print ''.join(f.read().split()) # Close the file.  f.close() # Slowly, now... f = open('anthrax_sasp.nuc') # Store the entire file's contents in s (as string) s = f.read() print s # Split s at whitespace sl = s.split() print sl # Join split s with nothing in between jl = ''.join(sl) print jl # Close the file f.close()
f = open('anthrax_sasp.nuc')
print f.read().split()
f.close()
s = f.read()
sl = s.split()
jl = ''.join(sl)
BCHB524 - Edwards

12. Files: Reading
# Open a file f = open('anthrax_sasp.nuc') # Iterate line-by-line for line in f:     print line # Close the file f.close() # Open a file f = open('anthrax_sasp.nuc') # Iterate line-by-line, and accumulate the sequence seq = "" for line in f:     seq += line.strip() print "The sequence is",seq # Close the file f.close()
f = open('anthrax_sasp.nuc')
print f.read().split()
f.close()
s = f.read()
sl = s.split()
jl = ''.join(sl)
BCHB524 - Edwards

13. DNA Translation First read a codon table from a file
Codon table from NCBI's on-line taxonomy resource
Read line by line and use initial word to store 3rd word appropriately.
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ---M M M
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
BCHB524 - Edwards

14. DNA Translation
f = open('standard.code') data = {} for l in f:     sl = l.split()     key = sl[0]     value = sl[2]     data[key] = value     f.close() b1 = data['Base1'] b2 = data['Base2'] b3 = data['Base3'] aa = data['AAs'] st = data['Starts'] codons = {} init = {} n = len(aa) for i in range(n):     codon = b1[i] + b2[i] + b3[i]     codons[codon] = aa[i]     init[codon] = (st[i] == 'M')
f = open('standard.code')
data = {}
for l in f:
sl = l.split()
key = sl[0]
value = sl[2]
data[key] = value
f.close()
b1 = data['Base1']
b2 = data['Base2']
b3 = data['Base3']
aa = data['AAs']
st = data['Starts']
codons = {}
init = {}
n = len(aa)
for i in range(n):
codon = b1[i] + b2[i] + b3[i]
codons[codon] = aa[i]
init[codon] = (st[i] == 'M')
BCHB524 - Edwards

15. DNA Translation
f = open('anthrax_sasp.nuc') seq = ''.join(f.read().split())
f.close() seqlen = len(seq) aaseq = [] for i in range(0,seqlen,3):     codon = seq[i:i+3]     aa = codons[codon]     aaseq.append(aa) print ''.join(aaseq)
f = open('standard.code')
data = {}
for l in f:
sl = l.split()
key = sl[0]
value = sl[2]
data[key] = value
f.close()
b1 = data['Base1']
b2 = data['Base2']
b3 = data['Base3']
aa = data['AAs']
st = data['Starts']
codons = {}
init = {}
n = len(aa)
for i in range(n):
codon = b1[i] + b2[i] + b3[i]
codons[codon] = aa[i]
init[codon] = (st[i] == 'M')
BCHB524 - Edwards

16. Exercise 1
Using just the concepts introduced so far, find as many ways as possible to code DNA reverse complement (at least 3!)
You may use any built-in function or string or list method.
You may use only basic data-types and lists and dictionaries.
Compare and critique each technique for robustness, speed, and correctness.
BCHB524 - Edwards

17. Exercise 2
Write a program that takes a codon table file (such as standard.code from the lecture) and a file containing nucleotide sequence (anthrax_sasp.nuc) as command-line arguments, and outputs the amino-acid sequence.
Modify your program to indicate whether or not the initial codon is consistent with the codon table's start codons.
Use NCBI's taxonomy resource to look up and download the correct codon table for the anthrax bacterium. Re-run your program using the correct codon table. Is the initial codon of the anthrax SASP gene a valid translation start site?
BCHB524 - Edwards

18. Homework 4 Due Monday, September 26. Submit using Canvas
Use only the techniques introduced so far.
Make sure you can run the programs demonstrated in lecture(s).
Exercises 1, 2 from Lecture 7
BCHB524 - Edwards