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
10
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")
11
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
12
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")
13
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")
14
Loops
condition
true
code
if
true
false
while
condition
block
of
code
to
execute
while
condition
is
true
15
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
16
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
17
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
18
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
19
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
20
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!
21
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=
22
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
23
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)
...
24
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)
...
25
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!
26
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
27
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
28
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)
29
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.
30
