1. while loops
Genome 559: Introduction to Statistical and Computational Genomics
Prof. William Stafford Noble

2. while loop statement1 statement2 while (<test>):
In English: While some logical test is true, continue executing the block of statements.

3. What does this program do?
sum = 0
count = 1
while (count < 3):
sum = sum + count
count = count + 1
print count
print sum

4. What does this program do?
sum = 0
count = 1
while (count < 3):
sum = sum + count
count = count + 1
print count
print sum
sum = 0
count = 1
count < 3? TRUE
sum = = 1
count = = 2
sum = = 3
count = = 3
count < 3? FALSE 3 3

5. Increment operator (+=)
x = x + y
is the same as
x += y
sum = 0
count = 1
while (count < 3):
sum = sum + count
count = count + 1
print count
print sum
sum = 0
count = 1
while (count < 3):
sum += count
count += 1
print count
print sum

6. For versus while loops You will probably use for loops more.
For is natural to loop through a list, characters in a string, etc. (anything of determinate size).
While is natural to loop an indeterminate number of times until some condition is met.

7. Examples of for loops for base in sequence:
<do something with each base>
for sequence in database:
<do something with each sequence>
for index in range(5,200):
<do something with each index>

8. Examples of while loops
while (error > 0.05):
<do something that will reduce error>
while (score > 0):
<traceback through a DP matrix, each time setting the current score>
Warning: if you write a while loop and the conditional test stays True, the loop will run forever (infinite loop).

9. Terminating a loop
while loops use continue and break in the same way as for loops:
continue : jumps to the top of the enclosing loop
break : breaks completely out of the enclosing loop

10. Sample problem #1 Convert the following program to a while loop:
import sys
total = 0
for i in range(1, len(sys.argv)):
total += int(sys.argv[i])
print total
Run both programs with arguments “1 2 3”.

11. Solution #1 import sys total = 0 i = 1 while (i < len(sys.argv)) :
total += int(sys.argv[i])
i += 1
print total

12. Sample problem #2
Write a python program to print all the square numbers up to a user- specified maximum:
> python print-squares.py 20 1 4 9 16
My solution has 6 lines.

13. Solution #2 import sys max_int = int(sys.argv[1]) index = 1
while (index * index < max_int):
print index * index
index += 1

14. Sample problem #3
Write a python program to count the lines in a file using readline() and a while loop.
> python count-lines.py myfile.txt 3
My solution has 8 lines.

15. Solution #3 import sys myfile = open(sys.argv[1], “r”) lineCount = 0
line = myfile.readline()
while (line != ""):
lineCount += 1
print lineCount

16. Sample problem #4
Write a program count-fasta.py that counts the number of fasta sequences in a file specified on the command line. Use either a while loop or a for loop.
python count-fasta.py small.fasta 72
23516
Run your program on the two files on the course web page: small.fasta and large.fasta.
Fasta format:
>identifier1 [optional comments]
AAOSIUBOASIUETOAISOBUAOSIDUGOAIBUOABOIUAS
AOSIUDTOAISUETOIGLKBJLZXCOITLJLBIULEIJLIJ
>identifier2 [optional comments]
TXDIGSIDJOIJEOITJOSIJOIGJSOIEJTSOE
>identifier3
Etc.
sequence on any number of lines until next line that starts with “>”

17. Solution #4 Not required, but a good habit to get into import sys
# Make sure we got an argument on the command line.
if (len(sys.argv) != 2):
print "USAGE: one file argument required"
sys.exit()
# Open the file for reading.
fasta_file = open(sys.argv[1], "r")
num_seqs = 0
for line in fasta_file:
# Increment if this is the start of a sequence
if (line[0] == ">"):
num_seqs += 1
fasta_file.close()
print num_seqs