1. Essential Computing for Bioinformatics
High-level Programming with Python
Iteration Over Sequences
MARC: Developing Bioinformatics Programs
Alex Ropelewski
PSC-NRBSC
Bienvenido Vélez
UPR Mayaguez
Reference: How to Think Like a Computer Scientist: Learning with Python

2. Essential Computing for Bioinformatics

3. Iterative Factorial Example
def iterFact(n):
result = 1
for i in xrange(1,n+1):
result = result * i
return result
xrange(start,end,step) generates a sequence of values :
The for loop is a somewhat less general iterative construct
Every for can be written as a while, yet for loops tend to be easier to read and understand.
For loops are recommended when we have an a priori list of values that we want to iterate over
Examples of such lists of values are:
Python lists or tuples
Discrete ranges of integer numbers
start = first value
end = value right after last one
step = increment
These materials were developed with funding from the US National Institutes of Health grant #2T36 GM to the Pittsburgh Supercomputing Center

4. Anatomy of the For Loop for <var> in <sequence>:
<block>
SYNTAX
Repeat the execution of the <block> binding variable <var> to each element of the sequence
SEMANTICS
These materials were developed with funding from the US National Institutes of Health grant #2T36 GM to the Pittsburgh Supercomputing Center

5. Complementing a DNA sequence
Write a Python function that takes a DNA sequences as an parameter and returns its complement:
Check validity of DNA sequence
Repeat for each nucleotide in sequence
Fetch the next nucleotide
Find its DNA complement nucleotide
Append the complement nucleotide to result sequence
Return the complement sequence

6. Complementing a DNA sequence
return result
return True
These materials were developed with funding from the US National Institutes of Health grant #2T36 GM to the Pittsburgh Supercomputing Center

7. Complementing a DNA sequence
from string import *
DNANucleotides='acgt'
DNAComplements='tgca'
raise Exception (" Invalid DNA sequence: " + n)
return (type(nucleotide) == type("") and
len(nucleotide)==1 and
nucleotide.lower() in DNANucleotides)
These materials were developed with funding from the US National Institutes of Health grant #2T36 GM to the Pittsburgh Supercomputing Center