Day_1.ipynb

Kernel: Python 2 (system-wide)

Variables

• Lets make a variable:

• Execute the code by pressing ctrl + enter

  • Name: first_name

  • Value: Aridaman

first_name = "Sander"
sur_name = "Boymans"
print first_name + " " + sur_name

Sander Boymans

Exercise:

• Print your surname using a new variable.

• Can you print both your first and surname?

number3=8/3.0
print number3

2.66666666667

Strings - methods

• All types have build in methods to manipulate them.

• For example:

  • my_string.upper() - returns the string in uppercase

# Write here your code

Exercise: Strings – Methods

• Assign a random number of DNA nucleotides to a variable.

• Print the DNA sequence in uppercase

• Count the number of A, C, G and T’s within the sequence

• Store these numbers in a new variable and print them

• Replace all A’s with T’s

• Time remaining?

  • Try other string methods

# Write here your code

Strings – Operators

• + Concatenate a string

• * Repetition of a string

• [n] Slice, returns nth value (Python counts from 0)

• [x:y] Range slice, returns the xth to yth value

• Not an operator but very useful:

  • len("ABCDEF") = 6

"ABC" + "DEF"

'ABCDEF'

"ABC" * 2

'ABCABC'

"ABCDEF"[3]

'D'

"ABCDEF"[2:4]

'CD'

len("ABCDEF")

6

Exercise: Strings – Operators

• Create two variables and assign a random number of DNA nucleotides to both.

• Combine both variables and print

• Add 10 copies of the second dna sequence to the combined sequence.

• Print the total length of the combined sequence

• Print the 5th nucleotide

• Print the 7th to the 14th nucleotide

• Bonus: print the last character of "gaattc" but not by using string[5]

# Write here your code

Strings - Special characters

• Tabs: \t

• Newlines: \n

• Quotes: "

• Backslash: \\

print "Tab\tTab\nSecond Line\nPrint out a \"backslash\" : \\"

Tab	Tab
Second Line
Print out a "backslash" : \

Comments

• Comments start with #

• Useful for:

  • Explaining code or your program

  • Disable parts of your program

# This is an example script using comments
print "Comment example script"
# print "This will not print"
print "This will print"

Comment example script
This will print

Last exercise on strings

• You can let Python ask you to input a variable:

  • your_name = raw_input("Please type your name:")

  • print your_name

• raw_input always returns a string!

• Let Python request your first and last name

• Print them using \t, \n, " and/or \\

• Play around with this for a couple minutes

your_name = raw_input("Please type your name:")
print your_name

# Write here your code

Numbers

• Integers: 1, 5, etc.

• Floats: 1.5, 5.2, etc.

• Simple math using numbers (x = 5.0 and y = 2.0) :

  • Addition: x + y = 7.0

  • Subtraction: x – y = 3.0

  • Division: x / y = 2.5

  • Multiplication: x * y = 10.0

  • Power: x ** y = 25.0

  • Modulo (remainder): x % y = 1.0 (2+2=4 5-4 = 1)

• Python uses the standard order of operations

  • 5 * (2+1) = 15

x = 5.0
y = 2.0

x + y

x - y

x / y

x * y

x ** y

x % y

5 * (2+1)

Numbers – Exercise

• Assign the value 8 to number1

• Assign the value 3 to number2

• Make number3 equal to the division of number1 by number2

• Print the number3

• Does the result make sense?

• Once it does, input a DNA sequence and calculate the GC %

# Write here your code

Converting types

• Sometimes we need to convert types

  • str(variable) converts variable to a string

  • int(variable) converts variable to a integer

  • float(variable) converts variable to a float

"2" + "2"

int("2") + int("2") 

str(2) + str(2) 

int("this does not work, why?")

float(5) / float(2) 

int(5.0) / int(2.0)

Last exercise on numbers

• Write a script that asks the user for

  • his/her name

  • length (m)

  • weight (kg)

• Calculate the bmi of the user

  • user_bmi = weight / length2

• Print out with one print command:

  • The used formula to calculate bmi and on the next line the name and bmi separated by a tab.

# Write here your code

Boolean: True or False

• Booleans are the outcome when you compare or test variables

• Examples:

x = 2
x < 3

x = "yes" 
x == "no"

Operators for comparison

• < less than

• <= less than or equal to

• > greater than

• >= greater than or equal to

• == equal

• != not equal

Boolean – exercise

• Below are a couple comparisons. Try to guess the result before executing the comparisons in python.

5 > 4

3 < 5

4 == 4

4 <= 4

4 >= 3

3 != 3

"yes" != "no"

"yes" == "yes"

Boolean – exercise

• Just like before, try to guess the result before executing the comparisons

5 > 3 and 5 > 1

5 < 3 or 5 > 1

not 5 > 3

False

not 5 > 3 or 5 > 1

True

not (5 > 3 or 5 > 1)

False

Control flow – if / else / elif

• With if, else and elif we can control the execution of certain parts of a program.

  • if (condition):

  • < tab > do something

• Example:

x = 5
if (x < 0): 
    print "x is negative"
elif (x > 0): 
    print "x is positive"
else: 
    print "x is 0"

Control flow – if – exercise

• Write a script that asks the user for a nucleotide

• Check whether the nucleotide is a adenine, thymine, cytosine or guanine

• Print out the nucleotide type or an error message if the input is not a nucleotide

# Write here your code

Loops – while

• while [removed]:

• < tab > do something

number = float(raw_input("Please provide a number: "))
while number < 20:
    print number
    number += 1

Loops – while – exercise

• Ask the user to enter some DNA sequence

• As long as the length of the DNA sequence is smaller than 100 keep the user asking for more DNA sequence and add it to the piece you already have

• Once you have more than 100 nucleotides print the result

# Write here your code

Loops – for

• for [removed] in [removed]:

• < tab > do something

string = "my string"
for char in string:
    print char

Loops – for – exercise

• Ask the user for a DNA code of exactly 10 nucleotides, and check this

• Using “for” start at nucleotide 1 and print one by one until and including nucleotide 5

• Time remaining?

• Ask the user for a random DNA code with a minimum length of 3 nucleotides and print the last 3 nucleotides going backwards

# Write here your code