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

for loop review for <element> in <object>: don’t forget the colon! for <element> in <object>: <statement> . . . <last statement> block of code <element> is a newly created variable name. You can access the variable after the loop completes. <object> is a container of one or more <element>s. It must already exist. range() will make a list of integers “on the fly” for index in range(0,100): <statement>

Choosing good variable names Pick names that are descriptive. Change a name if you decide there’s a better choice. (Use search and replace to be sure you don't miss any.) Very locally used names can be short and arbitrary The Python standard recommends using internal underscores rather than camelCase. list_of_lines = my_file.readlines() sequence = "GATCTCTATCT" my_DP_matrix = [[0,0,0],[0,0,0],[0,0,0]] sum = 0 for i in range(len(list_of_ints)): sum = sum + list_of_ints[i] (more code)

Comment liberally Any place a # sign appears, the rest of the line is a comment (ignored by program). Blank lines are also ignored – use them to visually group code. import sys query = sys.argv[1] my_file = open(sys.argv[2], "r") lines = my_file.readlines() # put all the lines from a file into a list # now process each file line to remove the \n character, then # search the line for query and record each result in a list of ints int_list = [] for line in lines: position = line.find(query) int_list.append(position) etc.

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

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

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 = 0 + 1 = 1 count = 1 + 1 = 2 sum = 1 + 2 = 3 count = 2 + 1 = 3 count < 3? FALSE 3 3

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

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.

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>

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).

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

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”.

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

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.

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

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.

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

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 “>”

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] == ">"): # parentheses are optional num_seqs += 1 fasta_file.close() print num_seqs