IFS

AND LOOPS
PYTHON FOR GENOMIC DATA SCIENCE

Decision Making
condition

false

true

code if
true

code if
false

if condition
block of code to execute if condition is true
else
other block of code to execute if condition is
false

The if Statement
Take a look at the following code:
>>> dna=input('Enter DNA sequence:')
Enter DNA sequence:agcgcgggtatatatatgcnccann
>>> if 'n' in dna :
nbases=dna.count('n')
print("dna sequence has %d undefined bases " % nbases)

dna sequence has 3 undefined bases

The if Statement
Take a look at the following code:
>>> dna=input('Enter DNA sequence:')
Enter DNA sequence:agcgcgggtatatatatgcnccann
condition
>>> if 'n' in dna :

block of code to execute if condition is true

nbases=dna.count('n')
print("dna sequence has %d undefined bases " % nbases)
notice the indentation that deHines the block
dna sequence has 3 undefined bases

Boolean Expressions
The condition in the if statement is called a Boolean

expression.
Boolean expressions are expressions that are either true or
false.
>>> 0<1
True
>>> len('atgcgt')>=10
False

Boolean expressions are formed with the help of

comparison, identity, and membership operators.

Comparison Operators
Comparison

Operator

>>> 'a'=='A'

Equal

==

False

Not equal

!=

>>> 'GT' != 'AG'

Less than

<

Greater than

>

Less than or
equal to

<=

Greater than
or equal to

>=

True

Do not confuse the assignment sign = with the comparison operator == !

Comparison Operators
Comparison

Operator

>>> 'a'=='A'

Equal

==

False

Not equal

!=

>>> 'GT' != 'AG'

Less than

<

True

Greater than

>

>>> 'A'<'C'

Less than or
equal to

<=

Greater than
or equal to

>=

True
>>> 10+1==11
True

Do not confuse the assignment sign = with the comparison operator == !

Membership Operators
Operator

Description

in

True if it Hinds a variable in the speciHied

sequence and false otherwise.

not in

True if it does not Hinds a variable in the

speciHied sequence and false otherwise.

>>> motif='gtccc'
>>> dna='atatattgtcccattt'
>>> motif in dna
True

Identity Operators
Operator

Description

is

True if the variables on either side of the operator point

to the same object and false otherwise.

is not

False if the variables on either side of the operator point

to the same object and true otherwise.

Identity Operators
Operator

Description

is

True if the variables on either side of the operator point

to the same object and false otherwise.

is not

False if the variables on either side of the operator point

to the same object and true otherwise.

>>> alphabet=[a,c,g,t]
>>> newalphabet=alphabet[:]
>>> alphabet == newalphabet
True
>>> alphabet is newalphabet
False
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Alternative Execution
check_dna.py
#!/usr/bin/python
dna=input('Enter DNA sequence:')
if 'n' in dna :
nbases=dna.count('n')
print("dna sequence has %d undefined bases " % nbases)
else:
print("dna sequence has no undefined bases")

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Multiple Alternative Executions

Sometimes it is convenient to test several conditions in one if structure.
if condition 1:
true
false
do action 1
condition1
elif condition 2:
false
true
condition2
do action 2
elif condition 3:
else
do action 3
if code
elif code
code

elif condition n:
do action n
else: # none of conditions 1,2,,n are true
do something else
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Multiple Alternative Executions (contd)

Sometimes it is convenient to test several conditions in one if structure.
check_dna.py
#!/usr/bin/python
dna=input('Enter DNA sequence:')
if 'n' in dna :
print("dna sequence has undefined bases ")
elif N in dna :
print("dna sequence has undefined bases ")
else:
print("dna sequence has no undefined bases")

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Logical Operators
and
or
not

- True if both conditions are true

- True if at least one condition is true
- True if condition is false

check_dna.py
#!/usr/bin/python
dna=input('Enter DNA sequence:')
if 'n' in dna or N in dna:
nbases=dna.count('n')+dna.count(N)
print("dna sequence has %d undefined bases " % nbases)
else:
print("dna sequence has no undefined bases")

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Loops

condition

true

code if
true

false

while condition
block of code to execute while condition is true

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The while Loop

Problem. Given a DNA sequence Hind the positions of all
canonical donor splice site candidates in the sequence.
Hind_donor.py
#!/usr/bin/python
dna=input('Enter DNA sequence:')
pos=dna.find('gt',0) # position of donor splice site

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The while Loop

Problem. Given a DNA sequence Hind the positions of all
canonical donor splice site candidates in the sequence.
Hind_donor.py
#!/usr/bin/python
dna=input('Enter DNA sequence:')
pos=dna.find('gt',0) # position of donor splice site
condition

block of code to execute while condition is true

while pos>-1 :
print("Donor splice site candidate at position %d%pos)
pos=dna.find('gt',pos+1)
notice the indentation that deHines the while block
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The for Loop

Pythons for loop iterates over the items of any sequence (a list
or a string), in the order that they appear in the sequence.
>>> motifs=["attccgt","agggggtttttcg","gtagc"]
iteration
variable

sequence to traverse

>>> for m in motifs:

...

print(m,len(m))

block of code to repeat for each

element

notice the indentation that deHines the for block

attccgt 7
agggggtttttcg 13
gtagc 5
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The range() Function

The range() built-in function allows you to iterate over a
sequence of numbers:
>>> for i in range(4):
...
print(i)
0
1
2
3
start stop

step

>> for i in range(1,10,2):

...
print(i)
1
3
5
7
9
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The range() Function (contd)

Problem. Find if all characters in a given protein sequence are
valid amino acids.
Pseudocode
for each character in protein sequence :
if character is not amino acid :
print invalid character and its position in protein
>>> protein='SDVIHRYKUUPAKSHGWYVCJRSRFTWMVWWRFRSCRA'
>>> for i in range(len(protein)):
...
if protein[i] not in 'ABCDEFGHIKLMNPQRSTVWXYZ':
...
print("protein contains invalid amino acid %s at
position %d"%(protein[i],i))
protein contains invalid amino acid U at position 8
protein contains invalid amino acid U at position 9
protein contains invalid amino acid J at position 20
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Breaking Out Of Loops

Problem. Suppose we are only interested in Hinding if a protein
sequence is valid, not where are all the invalid characters in the
sequence.
invalid amino acid character
>>> protein='SDVIHRYKUUPAKSHGWYVCJRSRFTWMVWWRFRSCRA'
>>> for i in range(len(protein)):
...

if protein[i] not in 'ABCDEFGHIKLMNPQRSTVWXYZ':

...

print(this is not a valid protein sequence!)

...

break

the break statement terminates the nearest

enclosing loop ( a for or while loop)

this is not a valid protein sequence!

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The continue Statement

The continue statement causes the program to continue with
the next iteration of the nearest enclosing loop, skipping the
rest of the code in the loop.
Problem. Delete all invalid amino acid characters from a protein
sequence.
>>> protein='SDVIHRYKUUPAKSHGWYVCJRSRFTWMVWWRFRSCRA'
>>> corrected_protein=

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The continue Statement

The continue statement causes the program to continue with
the next iteration of the nearest enclosing loop, skipping the
rest of the code in the loop.
Problem. Delete all invalid amino acid characters from a protein
sequence.
>>>
>>>
>>>
...
...
...
...
>>>

protein='SDVIHRYKUUPAKSHGWYVCJRSRFTWMVWWRFRSCRA'
corrected_protein=''
for i in range(len(protein)):
if protein[i] not in 'ABCDEFGHIKLMNPQRSTVWXYZ':
continue
corrected_protein=corrected_protein+protein[i]
print("Corrected protein sequence is:%s"%corrected_protein)

Corrected protein sequence is:SDVIHRYKPAKSHGWYVCRSRFTWMVWWRFRSCRA

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The continue Statement (contd)

Using the continue statement improves the readability of your
code:
for i in range(n):
if condition_1:
function_1(i)
if condition_2:
funtion_2(i)
if condition_3:
function_3(i)
...

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The continue Statement (contd)

Using the continue statement improves the readability of your
code:
for i in range(n):
if condition_1:
function_1(i)
if condition_2:
funtion_2(i)
if condition_3:
function_3(i)
...

for i in range(n):
if not condition_1:
continue
function_1(i)
if not condition_2:
continue
funtion_2(i)
if not condition_3:
continue
function_3(i)
...

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The else Statement Used With Loops

Loop statements may have an else clause.
If used with a for loop, the else statement is executed
when the loop has exhausted iterating the list.
If used with a while loop, the else statement is executed
when the condition becomes false.
The else statement is not executed if the loop is
terminated by the break statement!

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An Example Of Using else With A for Loop

Problem. Find all prime numbers smaller than a given integer.
>>> N=10
>>> for y in range(2, N):
...
for x in range(2, y):
...
if y % x == 0:
...
print(y, 'equals', x, '*', y//x)
...
break
...
else:
...
# loop fell through without finding a factor
...
print(y, 'is a prime number')
...
2 is a prime number
3 is a prime number
4 equals 2 * 2
5 is a prime number
6 equals 2 * 3
7 is a prime number
8 equals 2 * 4
9 equals 3 * 3
Solution adapted from https://docs.python.org/3/tutorial/controlflow.html

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An Example Of Using else With A for Loop

Problem. Find all prime numbers smaller than a given integer.
>>> N=10
>>> for y in range(2, N):
...
for x in range(2, y):
...
if y % x == 0:
...
print(y, 'equals', x, '*', y//x)
...
break
...
else:
...
# loop fell through without finding a factor
...
print(y, 'is a prime number')
...
2 is a prime number
3 is a prime number
4 equals 2 * 2
5 is a prime number
6 equals 2 * 3
7 is a prime number
8 equals 2 * 4
9 equals 3 * 3
Solution adapted from https://docs.python.org/3/tutorial/controlflow.html

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The pass Statement

Python's pass statement is a placeholder: it does nothing.
It is used when a statement is required syntactically but you

do not want any command or code to execute:

>>> if motif not in dna:
...
pass
... else:
...

some_function_here(motif,dna)

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The pass Statement

Python's pass statement is a placeholder: it does nothing.
It is used when a statement is required syntactically but you

do not want any command or code to execute:

>>> if motif not in dna:
...
pass
... else:
...

some_function_here(motif,dna)

Sometimes you can use the pass statement also when you

didnt yet write the code for a particular situation but you
need the placeholder so that the syntax of the rest of your
program is correct.
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