Python Terminology and Syntax

**Variable**-A variable is like a box storing a piece of data, giving a specific name to a value

A variable can be a string or a number

**String-**a string can contain letters, numbers and symbols and it MUST be within quotes (“a” or ‘a’)

A number can be an integer or a float

**Integer-**an integer is a number without a decimal point

**Float-**a float is a number with a decimal point

numbers can be used in mathematical expressions and are not contained within quotes

To set a variable

String >>> candy = “Twix”

Integer >>>a=7

Float >>>b=7.3

To change the value of a variable you can reassign it the same way you originally assigned it

>>>candy=”Snickers”

>>>a=3

>>>b=2.0

one equals sign (=) assigns a value to a variable

two equals signs (==) denotes equality

an exclamation point followed by a an equals sign (!=) means not equal

**Python Arithmetic**

In python you can perform mathematical operations on floats and numbers

**Addition** (+)

>>>2+2

Returns 4

>>>2.3+3.5

Returns 5.8

**Subtraction**(-)

>>>4-1

Returns 3

>>>3.3-2.2

Returns 1.1

**Multiplication** (*)

>>>7*3

Returns 21

>>>3.1*4.2

Returns 13.02

**Division** (/) is special,

An integer divided by an integer returns the quotient as an integer (without the decimals place) *rounded down*

>>>7/3

Returns 2

>>>15/4

Returns 3

A Float divided by a float returns the a float (with the decimals place)

>>>8.6/4.4

Returns 1.9545454545454544

>>>3.3/3.3

Returns 1.0

A float divided by an integer (or an integer divided by a float) returns a float (with the decimals place)

>>>3.3/2

Returns 1.65

>>>2/3.3

Returns 0.6060606060606061

To perform division with a float and return a whole number (still a float-ending in .0, also rounded down) you can use (//)

>>>3.3//3

Returns 1.0

**Exponentials **(**)

>>>6**3

Returns 4096

>>>6**2.0

Returns 36.0

**The Modulus** (%) Performs division and returns the remainder

>>>36%7

Returns 1

>>>100%80

Returns 20

>>36%8.6

Returns 1.6

** **

For more information on using python’s mathematical functions check out the python tutorial https://docs.python.org/2/tutorial/introduction.html#using-python-as-a-calculator

** **

**List-**A list is a variable that can hold multiple pieces of data at one time

A list can hold integers, floats and strings

You can even make lists of lists!

To create a list

>>>list_name=[‘string1’, ‘string2’, ‘string3’]

>>>Test_scores=[96, 83, 75]

>>>Celebs =[‘Beyoncé’, ‘Jay-Z, ‘Kanye’]

To access a particular list item use its **index-**a number indicating its place in the list

>>>print Celebs[2]

I bet you expected it to be Jay-Z, but in python (and I think most computer languages) the index starts at 0 (this is called 0-based numbering) so to print Jay-Z you would need to write >>>Celebs[1]

To add an item to a list

>>>list_name.append(‘new_item’)

Now

list_name=[‘string1’, ‘string2’, ‘string3’, ‘new_item’]

The new item is appended to the end of the list

>>>Celebs.append(‘Kim’)

Now

Celebs=[‘Beyoncé’, ‘Jay-Z, ‘Kanye’, ‘Kim’]

To remove a list item

>>>list_name.remove(‘new_item’)

Now

list_name=[‘string1’, ‘string2’, ‘string3’]

If ‘item’ occurred multiple times in the list, only the first occurrence would be removed

>>>Celebs.remove(‘Beyoncé’)

Now

Celebs=[‘Jay-Z, ‘Kanye’, ‘Kim’]

To change or replace a list item

>>>list_name[1]=’new_item’

Now

list_name=[‘string1’, ‘new_item’, ‘string3’]

This will replace the second item in the list with new_item

>>>Celebs[0]=’Kris’

Now

Celebs=[‘Kris, ‘Kanye’, ‘Kim’]

If you only want part of the list you can use **list slicing**

>>>list_name[a:b]

This will return items from a up to but not including b

>>>Celebs[0:2]

Would return ‘Kris’ and ‘Kanye’ (but not ‘Kim’)

If the first index is unspecified python will assume the slice begins at the beginning of the list

>>>Celebs[0:2]

will return the same thing as

>>>Celebs[:2]

If the second index is unspecified python will assume the slice ends at the end of the list

You can also include a third index

>>>list_name[a:b:c]

This tells python to include list items from a to b going by c (so if c was 2 it would include every other item)

For example if you had a list of numbers

>>>Numbers=[1,3,4,7,2,9,3,8,3,9,5,6,4,8,8]

and you wanted to return every other number from the 2^{nd} through 8^{th} positions

>>>Numbers[1:9:2]

Would return

[3,7,9,8]

You can also use a negative index to go backwards through the list

>>>Numbers[::-1]

Would return

[8, 8, 4, 6, 5, 9, 3, 8, 3, 9, 2, 7, 4, 3, 1]

String slicing works exactly the same way as list slicing (just replace the list_name with the string_name)

To count the number of times a particular item occurs in a list you can use the list_name.count() command

>>>Numbers.count(4)

Would return

2

This command also works for strings

>>>string_name.count(‘a’)

would return the number of times ‘a’ occurs in the string

For more information on lists check out the python tutorial https://docs.python.org/2/tutorial/datastructures.html

Sometimes the formatting on wordpress gets screwed up with different window sizes so I am also including screen shots (at the bottom of this post) of these commands and their results in the python shell.

Because I am using this blog as a repository for my programming notes as well as an educational/community building tool, I have decided to provide a more extensive documentation of python syntax then I had originally planed. However because I want to keep the focus of this blog on bioinformatics I am going to try to include a bioinformatics problem that is solvable with the syntax that has already been introduced. I will then post my solution to the problem at the top of the next blog post.

**The first bioinformatics problem!**

Write a program to count the number of each base (ATCG) and the number of ambiguities(N) in the given nucleotide sequence

nt_sequence

Don’t forget python is case sensitive

Feel free to post your solution, or any questions in the comments section.

Good Luck!

From the functions you’ve used, I guess your solution involves finding the difference between lengths of original and nucl-trimmed strings, amirite?