Download condition - Computational Approaches for Life Scientists

Computational Approaches
for Life Scientists
Faculty of Biology
Technion
Spring 2013
Amir Rubinstein
Python basics 2
Outline
• Python basics:
• types in Python
• input and output
• operators
• functions
• conditions
• loops – while, for
• sequences:
- strings
- lists
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Getting started with Python
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Let's see some real Python first
dna = input("please enter a dna sequence\n")
A = dna.count("A")
T = dna.count("T")
C = dna.count("G")
G = dna.count("C")
print ( 100*(C+G)/(A+T+C+G) )
def ambiguous_bases_count(dna):
amb = 0 #bases != a,t,g,c
for base in dna:
if base not in "atgc":
amb += 1
return amb
def check_dna(dna, alphabet="atgc"):
for base in dna:
if base not in alphabet:
return False
return True
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Let's see some real Python first
standard = {
'ttt': 'F',
'ttc': 'F',
'tta': 'L',
'ttg': 'L',
'ctt': 'L',
'ctc': 'L',
'cta': 'L',
'ctg': 'L',
'att': 'I',
'atc': 'I',
'ata': 'I',
'atg': 'M',
'gtt': 'V',
'gtc': 'V',
'gta': 'V',
'gtg': 'V',
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'tct':
'tcc':
'tca':
'tcg':
'cct':
'ccc':
'cca':
'ccg':
'act':
'acc':
'aca':
'acg':
'gct':
'gcc':
'gca':
'gcg':
'S',
'S',
'S',
'S',
'P',
'P',
'P',
'P',
'T',
'T',
'T',
'T',
'A',
'A',
'A',
'A',
'tat':
'tac':
'taa':
'tag':
'cat':
'cac':
'caa':
'cag':
'aat':
'aac':
'aaa':
'aag':
'gat':
'gac':
'gaa':
'gag':
'Y',
'Y',
'*',
'*',
'H',
'H',
'Q',
'Q',
'N',
'N',
'K',
'K',
'D',
'D',
'E',
'E',
'tgt':
'tgc':
'tca':
'tcg':
'cgt':
'cgc':
'cga':
'cgg':
'agt':
'agc':
'aga':
'agg':
'ggt':
'ggc':
'gga':
'ggg':
'C',
'C',
'*',
'W',
'R',
'R',
'R',
'R',
'S',
'S',
'R',
'R',
'G',
'G',
'G',
'G'
}
def dna_translate(cdna, code=standard):
""" translate a cDNA sequence to a protein """
prot = ""
for i in range(0,len(cdna),3):
prot += code.get(cdna[i:i+3], "?")
return prot
Let’s run (some code)!
•
You can find all these pieces of code on the website – in the file basics.py
•
Opening .py files for editing:
•
•
right click  edit with IDLE
•
double click will not open the file, just run the program
Running py files:
•
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after opening, Run  Run Module (or press F5)
Interactive (shell) vs. Script mode
•
When we open IDLE we get the shell mode,
also called Interactive mode .
This is a "ping-pong" mode.
we can run 1 command at a time.
Very convinient for short calculations.
•
script mode enables writing the whole program first, saving it in a .py
file, and only then running it line by line.
to work in script mode:
1. File  New Window
2. write your program
3. Run  Run Module (F5)
You will be asked to save your program.
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Make sure the file name ends with .py
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Basic types in python
•
Python has classes, or types of objects.
An instance is a specific object of a class. Instances of the same class
share some common features.
type
meaning
int
•
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Integers
float
Real numbers
bool
Boolean
Examples for instance
…, -3, -2, -1, 0, 1, 2, 3, …
x
3.14, -0.001 , …
True, False
str
String (sequence of
characters)
list
Sequence of
elements
func
Function
"amir", "!" , "45", "3.14" , …
flag
msg
[ 1, "hello" , -0.25, False, ["a", "b"] ]
grades
print, input, len, …
Variables are names given to objects.
x=5
flag = True
msg = “hello”
grades = [90, 85, 99, 76, 31]
Basic types in python
•
To check the type of an object, we can use the function type(…).
>>> type(6)
<class 'int'>
>>> x=5.7
>>> type(x)
<class 'float'>
>>> type("biology")
<class 'str'>
>>> type([4,5,"DNA", x])
<class 'list'>
•
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In Python, types can change (not only values)!
>>> x=5.7
>>> type(x)
<class 'float'>
>>> x="drosophila"
>>> type(x)
<class 'str'>
Type conversions
•
Python allows any “reasonable” type conversion.
using conversion functions such as:
int(), float(), str(), list(), …
>>> int("6")
6
>>> int(6.7) #rounds down
6
>>> float("3.14")
3.14
>>> str(45)
'45'
>>> int("a")
Traceback (most recent call last):
File "<pyshell#64>", line 1, in <module>
int("a")
ValueError: invalid literal for int() with base 10: 'a'
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The functions input(…) and print(…)
>>> print("Hello")
Hello
>>> print("Hello", "class!")
Hello class!
>>> course = "'Comp. App. for Life Scientists'"
>>> print("Hello", course, "students")
Hello 'Comp. App. for Life Scientists' students
>>> name = input("What's your name? ")
What's your name? Amir
>>> print(name, type(name))
Amir <class 'str'>
>>> grade = int(input("What's your grade? "))
What's your grade? 90
new = min(100, round(1.05*grade))
>>> print("Factorized grade is", new, "!")
Factorized grade is 95 !
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input(…) always
returns a string
Numerical operators
operator
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meaning
Examples
-
unary minus
-5
+
plus
x+7
-
binary minus
6-y
*
multiplication
x*y
/
float division
28/10 = 2.8
//
int division
28//10 = 2
%
modulo
10%2 = 0
**
power
2**10 = 1024
Let’s run (some code)!
write a program (in script mode) that gets a temperature in Celcius, and
prints the temperature in Fahrenheit.
The formula: ºF = ºC*1.8 + 32
See the next slide on functions.
Now turn your program into a function, run* the code and call your
function.
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* after pressing F5 – a shell windown should be opened, but no commands
should be executed, until you actually call you function.
Functions
def func_name (parameters) :
<-tab-> statement
statement
…
function executes
until the first
return statement
dna = input("please enter a dna sequence\n")
A = dna.count("A")
T = dna.count("T")
program calls
C = dna.count("G")
built-in functions:
G = dna.count("C")
input, count, print
print ( 100*(C+G)/(A+T+C+G) )
make sure you
still remember
and understand
why using
functions is
good.
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def GC_content(dna):
"""calculate CG% in string dna"""
A = dna.count("A")
user-defined
T = dna.count("T")
function calls builtC = dna.count("G")
in function count)
G = dna.count("C")
return 100*(C+G)/(A+T+C+G)
Function classification
•
functions can be diveded into these categories:
•
user-defined
def func_name :
…
•
built-in
come "free" with python
print, input, type, int, float,…
some built-in functions are bound
to some class.
example: dna.count(…)
the function count(…) of class str.
•
imported
will see this soon.
requires import statement.
(like #include in C)
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Conditionals
if condition :
<-tab-> statement
statement
…
elif condition :
# 0 or more
<-tab-> statement
…
else:
# optional
<-tab-> statement
…
Can use these operators in the
conditions:
comparison operators:
==, !=, >, <, >=, <=
logical operator:
and, or, not
write a function that gets the room temperature, and three state transition
temperatures of a polymer:
Tg (glass transition), Tm (melting), Tv (vaporization).
The function will print the state of the polymer: solid or liquid.
if in solid state, also print glassy state: glassy (< Tg) or rubbery .
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A word about tabs
•
In python, tabs are very important!
•
they determine the scope.
•
Tip: take care when copying-pasting from other sources.
sometimes the code will not work because tabs were ruined.
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Sequences
•
Sequences are highly important in our biological context.
•
We mentioned so far 2 kinds of sequences:
-
Strings (sequences of characters)
multi lines:
"GCTTA" or 'GCTTA'
"""GTAT
GGTA
TCCG"""
•
Lists (sequences of any instances)
There are some common properties to strings and lists (and other sequences).
We’ll se these first, and then some differences.
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[1, 2, 3]
Strings and Lists commonalities
-
Some built-in python function
are applicable to both str and list:
len(seq)
min(seq)
max(seq)
-
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indexing :
seq[i] 0≤i<len(seq)
including higher dimension indexing:
seq[i][j][…]
-
slicing:
seq[a:b:c]
-
membership test:
element in seq
-
concatenation (+)
seq1 + seq2
-
duplication (*)
seq * int
-
comparison (==)
seq1 == seq2
seq1 != seq2
Strings and Lists commonalities (2)
•
loops: we can iterate over a sequence using a for loop.
for name in sequence :
<-tab-> statement
statement
…
statement #out of loop
…
name is assigned
sequences element
one by one.
def countA(dna):
cntA = 0
for base in dna:
if base == "A":
cntA += 1
return cntA
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Loops: for and while
for name in sequence :
<-tab-> statement
statement
…
statement #out of loop
…
def countA(dna):
cntA = 0
for base in dna:
if base == "A":
cntA += 1
return cntA
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while condition :
<-tab-> statement
statement
…
statement #out of loop
…
def countA(dna):
cntA = 0
i=0
while i < len(dna):
if dna[i] == "A":
cntA += 1
i += 1
return Acnt
One of the statement must
affect the condition
(what would happen if not?)
Strings and Lists differences
•
Strings consist only of characters. Lists consist anything.
•
lists are mutable (we can mutate their inner elements)
strings are immutable.
>>> dna = "AGGACGATTAGACG"
>>> dna[4] = "G"
Traceback (most recent call last):
File "<pyshell#43>", line 1, in <module>
dna[4] = "G"
TypeError: 'str' object does not support item assignment
>>> Glycine = ["GGU", "GGC", "GGA", "GGg"]
>>> Glycine[3][2] = "G"
Traceback (most recent call last):
File "<pyshell#45>", line 1, in <module>
Glycine[3][2] = "G"
TypeError: 'str' object does not support item assignment
>>> Glycine[3] = "GGG"
>>> Glycine
['GGU', 'GGC', 'GGA', 'GGG']
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Strings and Lists differences (2)
•
Each of these types has its own functions that are bound to it.
You can get to list of a type's available functions using:
-
help command on that type
-
manuals and sources on the web
-
or simply by typing the name of a class (or an instance of it) followed by a
dot (.), and then tab.
a list of functions bound to that class will open.
•
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However there are functions in both classes: count(…) and index(…)
Conversion between lists and strings
•
Converting str to list is easy:
>>> list("TATAAA")
['T', 'A', 'T', 'A', 'A', 'A']
•
What about the opposite?
>>> str(['T', 'A', 'T', 'A', 'A', 'A'])
"['T', 'A', 'T', 'A', 'A', 'A']"
not exactly what we expected.
solution: str class has a function join:
seperator_string.join(list_of_characters)
>>> "w".join(['T', 'A', 'T', 'A', 'A', 'A'])
'TwAwTwAwAwA'
>>> "".join(['T', 'A', 'T', 'A', 'A', 'A'])
'TATAAA'
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Exercise
Generalize the GC_content function.
instead of getting 1 parameter and returning the CG%, it should get two
parameters:
-
seq: a string representing DNA / protein or any other sequence
-
items: a list containing characters we want to count.
the function should return the total % of all the characters in the list.
>>> count("TATTA", ["T"])
60.0
>>> count("TATTA", ["t", "T"])
60.0
>>> count("TATTA", ["t", "a", "g", "c"])
0.0
>>> count("RPKPQQFFGLM", ["Q", "F"])
36.36363636363637
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What's left (Python basics)?
-
files
-
dictionaries
-
libraries and import
One can go on and develop expertese in Python.
This is not our goal in this course.
But make sure you feel comfortable with what we've learned.
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What to do after this class - reminder
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