The document provides information on various Python programming concepts including control structures, lists, dictionaries, regular expressions, exceptions, and biological applications using Biopython. It discusses if/else statements, while and for loops, list operations, dictionary usage, regex patterns, exception handling roles, and gives examples analyzing protein sequences and structures using Biopython.

2. FBW
28-11-2017
Wim Van Criekinge

3. Google Calendar

5. Control Structures
if condition:
statements
[elif condition:
statements] ...
else:
statements
while condition:
statements
for var in sequence:
statements
break
continue

6. Lists
• Flexible arrays, not Lisp-like linked
lists
• a = [99, "bottles of beer", ["on", "the",
"wall"]]
• Same operators as for strings
• a+b, a*3, a[0], a[-1], a[1:], len(a)
• Item and slice assignment
• a[0] = 98
• a[1:2] = ["bottles", "of", "beer"]
-> [98, "bottles", "of", "beer", ["on", "the", "wall"]]
• del a[-1] # -> [98, "bottles", "of", "beer"]

7. Dictionaries
• Hash tables, "associative arrays"
• d = {"duck": "eend", "water": "water"}
• Lookup:
• d["duck"] -> "eend"
• d["back"] # raises KeyError exception
• Delete, insert, overwrite:
• del d["water"] # {"duck": "eend", "back": "rug"}
• d["back"] = "rug" # {"duck": "eend", "back":
"rug"}
• d["duck"] = "duik" # {"duck": "duik", "back":
"rug"}

8. Regex.py
text = 'abbaaabbbbaaaaa'
pattern = 'ab'
for match in re.finditer(pattern, text):
s = match.start()
e = match.end()
print ('Found "%s" at %d:%d' % (text[s:e], s, e))
m = re.search("^([A-Z]) ",line)
if m:
from_letter = m.groups()[0]

9. Install Biopython
pip is the preferred installer program.
Starting with Python 3.4, it is included
by default with the Python binary
installers.
pip3.5 install Biopython
#pip3.5 install yahoo_finance
from yahoo_finance import Share
yahoo = Share('AAPL')
print (yahoo.get_open())

11. Prelude
• Erdos
• Gaussian - towards random
DNAwalks
• Fetch random Protein
• AAindex parser

12. Erdos.py

14. Gaussian.py

15. Prelude
• Erdos
• Gaussian - towards random
DNAwalks
• Fetch random Protein
• AAindex parser

17. To be adapted for proteins …

18. Exceptions
• Exceptions are events that can modify the
flow or control through a program.
• They are automatically triggered on errors.
• try/except : catch and recover from raised
by you or Python exceptions
• try/finally: perform cleanup actions
whether exceptions occur or not
• raise: trigger an exception manually in
your code
• assert: conditionally trigger an exception
in your code

19. Exception Roles
• Error handling
– Wherever Python detects an error it raises
exceptions
– Default behavior: stops program.
– Otherwise, code try to catch and recover from the
exception (try handler)
• Event notification
– Can signal a valid condition (for example, in
search)
• Special-case handling
– Handles unusual situations
• Termination actions
– Guarantees the required closing-time operators
(try/finally)
• Unusual control-flows
– A sort of high-level “goto”

20. Example

22. Prelude
• Erdos
• Gaussian - towards random
DNAwalks
• Fetch random Protein
• AAindex parser

24. BioPython
• Make a histogram of the MW (in kDa) of all proteins in
Swiss-Prot
• Find the most basic and most acidic protein in Swiss-Prot?
• Biological relevance of the results ?
From AAIndex
H ZIMJ680104
D Isoelectric point (Zimmerman et al., 1968)
R LIT:2004109b PMID:5700434
A Zimmerman, J.M., Eliezer, N. and Simha, R.
T The characterization of amino acid sequences in proteins by
statistical
methods
J J. Theor. Biol. 21, 170-201 (1968)
C KLEP840101 0.941 FAUJ880111 0.813 FINA910103 0.805
I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
6.00 10.76 5.41 2.77 5.05 5.65 3.22 5.97 7.59 6.02
5.98 9.74 5.74 5.48 6.30 5.68 5.66 5.89 5.66 5.96

25. Find_Most_Basic_Protein.py

26. Find_Most_Basic_Protein.py

28. Extra Questions
• How many human proteins in Swiss Prot ?
• What is the longest human protein ? The shortest ?
• Calculate for all human proteins their MW and pI, display as
two histograms (2D scatter ?)
• How many human proteins have “cancer” in their description?
• Which genes has the highest number of SNPs/somatic
mutations (COSMIC)
• How many human DNA-repair enzymes are represented in
Swiss Prot (using description / GO)?
• List proteins that only contain alpha-helices based on the
Chou-Fasman algorithm
• List proteins based on the number of predicted
transmembrane regions (Kyte-Doollittle)

30. Biopython AAindex ? Dictionary
Hydrophobicity = {A:6.00,L:5.98,R:10.76,K:9.74,N:5.41,M:5.74,D:2.77,F:5.48,
C:5.05,P:6.30,Q:5.65,S:5.68,E:3.22,T:5.66,G:5.97,W:5.89,
H:7.59,Y:5.66,I:6.02,V:5.96}
from Bio import SeqIO
c=0
handle = open(r'/Users/wvcrieki/Downloads/uniprot_sprot.dat')
for seq_rec in SeqIO.parse(handle, "swiss"):
print (seq_rec.id)
print (repr(seq_rec.seq))
print (len(seq_rec))
c+=1
if c>5:
break

31. Extra Questions (2)
• How many human proteins in Swiss Prot ?
• What is the longest human protein ? The shortest ?
• Calculate for all human proteins their MW and pI, display as
two histograms (2D scatter ?)
• How many human proteins have “cancer” in their description?
• Which genes has the highest number of SNPs/somatic
mutations (COSMIC)
• How many human DNA-repair enzymes are represented in
Swiss Prot (using description / GO)?
• List proteins that only contain alpha-helices based on the
Chou-Fasman algorithm
• List proteins based on the number of predicted
transmembrane regions (Kyte-Doollittle)

32. Primary sequence reveals important clues about a protein
DnaG E. coli ...EPNRLLVVEGYMDVVAL...
DnaG S. typ ...EPQRLLVVEGYMDVVAL...
DnaG B. subt ...KQERAVLFEGFADVYTA...
gp4 T3 ...GGKKIVVTEGEIDMLTV...
gp4 T7 ...GGKKIVVTEGEIDALTV...
: *: :: * * : :
small hydrophobic
large hydrophobic
polar
positive charge
negative charge
• Evolution conserves amino acids that are important to protein
structure and function across species. Sequence comparison of
multiple “homologs” of a particular protein reveals highly
conserved regions that are important for function.
• Clusters of conserved residues are called “motifs” -- motifs
carry out a particular function or form a particular structure
that is important for the conserved protein.
motif

33.  The hydropathy index of an amino acid is a number
representing the hydrophobic or hydrophilic properties of its
side-chain.
 It was proposed by Jack Kyte and Russell Doolittle in 1982.
 The larger the number is, the more hydrophobic the amino
acid. The most hydrophobic amino acids are isoleucine (4.5)
and valine (4.2). The most hydrophilic ones are arginine (-4.5)
and lysine (-3.9).
 This is very important in protein structure; hydrophobic
amino acids tend to be internal in the protein 3D structure,
while hydrophilic amino acids are more commonly found
towards the protein surface.
Hydropathy index of amino acids

34. (http://gcat.davidson.edu/DGPB/kd/kyte-doolittle.htm)Kyte Doolittle Hydropathy Plot

35. Possible transmembrane fragment

36. Window size – 9, strong negative peaks indicate possible surface regions
Surface region of a protein

37. Prediction of transmembrane helices in proteins
(TMHMM)

38. 5-hydroxytryptamine receptor 2A (Mus musculus)

39. 5-hydroxytryptamine receptor 2 (Grapical output)