introduction to python programming -...
TRANSCRIPT
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Introduction to Python Programming
Luis Pedro Coelho§
On the web: http://luispedro.orgOn twitter: @luispedrocoelho
European Molecular Biology Laboratory
June 10, 2014
Luis Pedro Coelho ([email protected]) (EMBL) ⋆ Python I ⋆ June 10, 2014 (1 / 36)
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Python
Let’s digress for a moment discussing the language…
Luis Pedro Coelho ([email protected]) (EMBL) ⋆ Python I ⋆ June 10, 2014 (2 / 36)
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Python Language History
HistoryPython was started in the late 80’s.It was intended to be both easy to teach and industrial strength.It is (has always been) open-source.In the last 10 years, it has become one of the most widely usedlanguages (top 10).
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Python Versions
Python VersionsThe current versions of Python are 2.7 and 3.4This class assumes you have 2.6–2.7There are some small differences when compared to version 3.x
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What is a Computer?
...1 Memory
...2 Processor
...3 Magic
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Python Model
...1 Objects
...2 Operations on objects
...3 Magic
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Python Example
pr in t ” He l lo World”
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Running Python...1 From a file...2 Interactively
Luis Pedro Coelho ([email protected]) (EMBL) ⋆ Python I ⋆ June 10, 2014 (10 / 36)
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Computer Program
helloword.pypr in t ’ He l l o World ’
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Running a Program
...1 Shell
...2 IDE
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Let me show you a demonstration…
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More Complex Example
What is 25 times 5?
pr in t 25 * 5
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More Complex Example
What is 25 times 5?pr in t 25 * 5
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More Complex Example
name = 2other = 3yetanother = name + othername = 5pr in t yetanother + name
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Blackboard demonstration
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Conditionals
i f <cond i t i on>:<statement 1><statement 2>
e l s e :<statement 3>
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Conditionals (Example)
pr in t ’ Before t e s t i n g . . . ’i f 3 . 3*9 . 2 > 30 :
p r i n t ’ Greater than 30 ’e l s e :
p r i n t ’ Smal ler or equal ’p r i n t ’ After ’
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Conditionals (Example)
pr in t ’ Before t e s t i n g . . . ’i f 3 . 3*9 . 2 > 31 :
p r i n t ’ Greater than 31 ’e l i f 3 . 3*9 . 2 > 30 :
p r i n t ’ Greater than 30 ’e l s e :
p r i n t ’ Smal ler or equal ’p r i n t ’ After ’
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Conditionals (Example)
pr in t ’ Before t e s t i n g . . . ’v = 3 . 3*9 . 2i f v > 31 :
p r i n t ’ Greater than 31 ’e l i f v > 30 :
p r i n t ’ Greater than 30 ’e l s e :
p r i n t ’ Smal ler or equal ’p r i n t ’ After ’
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Lists
s tudents = [ ’ Luis ’ , ’Mark ’ , ’ Rita ’ ]
p r i n t s tudents [ 0 ]p r i n t s tudents [ 1 ]p r i n t s tudents [ 2 ]
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Loops
s tudents = [ ’ Luis ’ , ’Mark ’ , ’ Rita ’ , . . . ]
f o r s t in s tudents :p r i n t s t
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Example
va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
sum = 0f o r v in va lue s :
sum = sum + vpr in t sum
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Example
va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
sum = 0f o r v in va lue s :
sum = sum + vpr in t sum
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Exercise
How do you obtain the number of elements in a list?Use this to compute the mean of a list of numbers
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Example
va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
sum = 0 . 0sum2 = 0 . 0f o r v in va lue s :
sum = sum + vsum2 = sum2 + v * v
mu = sum/ len ( va lue s )mu2 = sum2/ l en ( va lue s )p r i n t ’ Average : {0} ’ . format (mu)p r in t ’ Std Dev : {0} ’ . format (mu2 - mu*mu)
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Example
va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
sum = 0 . 0sum2 = 0 . 0f o r v in va lue s :
sum += vsum2 += v * v
mu = sum/ len ( va lue s )mu2 = sum2/ l en ( va lue s )p r i n t ’ Average : {0} ’ . format (mu)p r in t ’ Std Dev : {0} ’ . format (mu2 - mu*mu)
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Example
va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
mu = 0 . 0mu2 = 0 . 0f o r v in va lue s :
mu += vmu2 += v * v
mu /= len ( va lue s )mu2 /= len ( va lue s )p r i n t ’ Average : {0} ’ . format (mu)p r in t ’ Std Dev : {0} ’ . format (mu2 - mu*mu)
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Example
va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
mu = 0 . 0mu2 = 0 . 0f o r v in va lue s :
mu += vmu2 += v * v
mu /= len ( va lue s )mu2 /= len ( va lue s )p r i n t ’ Average : {0} ’ . format (mu)p r in t ’ Std Dev : {0} ’ . format (mu2 - mu*mu)
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ExerciseAdapt the code to ignore negative numbers.
va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
mu = 0 . 0mu2 = 0 . 0n = 0 . 0f o r v in va lue s :
i f v >= 0 . 0 :mu += vmu2 += v * vn += 1
mu /= nmu2 /= npr in t ’ Average : {0} ’ . format (mu)p r in t ’ Std Dev : {0} ’ . format (mu2 - mu*mu)
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ExerciseAdapt the code to ignore negative numbers.va lue s = [ 0 . 11 , - 0 . 23 , - 0 . 16 , 0 . 18 , 0 . 23 , 0 . 19 ]
mu = 0 . 0mu2 = 0 . 0n = 0 . 0f o r v in va lue s :
i f v >= 0 . 0 :mu += vmu2 += v * vn += 1
mu /= nmu2 /= npr in t ’ Average : {0} ’ . format (mu)p r in t ’ Std Dev : {0} ’ . format (mu2 - mu*mu)
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Loops (II)Greatest Common Divisor (Euclid’s Method)
gcd(a,b) =
a if b = agcd(a− b,b) if a > bgcd(a,b− a) o.w.
a = 9344b = 6497
whi l e a != b :i f a > b :
a , b = a -b , be l s e :
a , b = a , b - ap r i n t a
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Loops (II)Greatest Common Divisor (Euclid’s Method)
gcd(a,b) =
a if b = agcd(a− b,b) if a > bgcd(a,b− a) o.w.
a = 9344b = 6497
whi l e a != b :i f a > b :
a , b = a -b , be l s e :
a , b = a , b - ap r i n t a
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Python So Far
Python...1 Basic types: int, float, list...2 Control flow: for, while, if, else, elif
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List Indexing
s tudents = [ ’ Luis ’ , ’ Rita ’ , ’ Sabah ’ , ’ Grace ’ ]p r i n t s tudents [ 0 ]p r i n t s tudents [ 1 : 2 ]p r i n t s tudents [ 1 : ]p r i n t s tudents [ - 1 ]p r i n t s tudents [ - 2 ]
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Tuples (I)
A = (0 , 1 , 2 )B = (1 , )
p r i n t A[ 0 ]p r i n t l en (B)
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Tuples (II)
Tuples are like immutable lists.
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Dictionaries
Dictionaries are associative arrays.
gene2ensembl = {}gene2ensembl [ ’SMAD9’ ] = ’ENSG00000120693 ’gene2ensembl [ ’ZNF670 ’ ] = ’ENSG00000135747 ’
p r i n t gene2ensembl [ ’SMAD9’ ]
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Dictionary Methods
gene2expre s s i on = {’SMAD9’ : 12 . 3 ,’ZNF670 ’ : 4 . 3 ,
}
p r i n t l en ( gene2ensembl )p r i n t gene2ensembl . keys ( )
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