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assignment2_dna_processing.py
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assignment2_dna_processing.py
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def get_length(dna):
""" (str) -> int
Return the length of the DNA sequence dna.
>>> get_length('ATCGAT')
6
>>> get_length('ATCG')
4
"""
count_sequence = 0
for n in dna:
count_sequence = count_sequence + 1
return count_sequence
def is_longer(dna1, dna2):
""" (str, str) -> bool
Return True if and only if DNA sequence dna1 is longer than DNA sequence
dna2.
>>> is_longer('ATCG', 'AT')
True
>>> is_longer('ATCG', 'ATCGGA')
False
"""
return get_length(dna1) > get_length(dna2)
def count_nucleotides(dna, nucleotide):
""" (str, str) -> int
Return the number of occurrences of nucleotide in the DNA sequence dna.
>>> count_nucleotides('ATCGGC', 'G')
2
>>> count_nucleotides('ATCTA', 'G')
0
"""
count_nucleotide = 0
for n in dna:
if n == nucleotide:
count_nucleotide = count_nucleotide + 1
return count_nucleotide
def contains_sequence(dna1, dna2):
""" (str, str) -> bool
Return True if and only if DNA sequence dna2 occurs
in the DNA sequence dna1.
>>> contains_sequence('ATCGGC', 'GG')
True
>>> contains_sequence('ATCGGC', 'GT')
False
"""
return (dna2 in dna1)
def is_valid_sequence(dna):
''' (str) -> bool
Return True if DNA sequence dna1 is valid, that is
it contains only characters, 'A', 'T', 'C', 'G'
>>> is_valid_sequence('atcg')
Fasle
>>> is_valid_sequence('ATC')
True
>>> is_valid_sequence('ATCH')
False
'''
if dna.islower():
return False
valid_nucleotides = 'ATCG'
for n in dna:
if n not in valid_nucleotides:
return False
return True
def insert_sequence(dna1, dna2, i):
''' (str, str, int) -> str
Return the DAN sequence obtained by inserting the seconds DNA dna2 into
the first DAN sequence dna1 at the given index i.
>>> insert_sequence('CCGG', 'AT', 2)
CCATGG
>>> insert_sequence('CCGG', 'AT', 0)
ATCCGG
>>> insert_sequence('CCGG' , 'AT', len('CCGG')-1)
CCGATG
>>> insert_sequence('CCGG', 'AT', -2)
CCATGG
>>> insert_sequence('CCGG', 'AT', -1)
CCGATG
'''
return dna1[:i] + dna2 + dna1[i:]
def get_complement(nucleotide):
''' (str)-> str
Return the nucleotide's complement
>>> get_complement('A')
T
>>> get_complement('T')
A
>>> get_complement('C')
G
>>> get_complement('G')
C
'''
n_complement =''
if nucleotide in 'A':
n_complement = 'T'
elif nucleotide in 'T':
n_complement = 'A'
elif nucleotide in 'C':
n_complement = 'G'
else:
n_complement = 'C'
return n_complement
def get_complementary_sequence(dna):
''' (str) -> str
Return the complementary sequence of the DNA dna
>>> get_complementary_sequence('AT')
TA
>>> get_complementary_sequence('GC')
CG
'''
dna_complement = ''
for n in dna:
dna_complement = dna_complement + get_complement(n)
return dna_complement