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gene_finder.py
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gene_finder.py
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# -*- coding: utf-8 -*-
"""
YOUR HEADER COMMENT HERE
@author: Chenlin (Harry) Liu
"""
import random
from amino_acids import aa, codons, aa_table # you may find these useful
from load import load_seq
def shuffle_string(s):
"""Shuffles the characters in the input string
NOTE: this is a helper function, you do not
have to modify this in any way """
return ''.join(random.sample(s, len(s)))
# YOU WILL START YOUR IMPLEMENTATION FROM HERE DOWN ###
def get_complement(nucleotide):
""" Returns the complementary nucleotide
nucleotide: a nucleotide (A, C, G, or T) represented as a string
returns: the complementary nucleotide
>>> get_complement('A')
'T'
>>> get_complement('C')
'G'
>>> get_complement('T')
'A'
>>> get_complement('G')
'C'
"""
nu_AT_swap = nucleotide.replace('A', 'K').replace('T', 'A').replace('K', 'T')
nu_CG_swap = nu_AT_swap.replace('C', 'S').replace('G', 'C').replace('S', 'G')
return nu_CG_swap
def get_reverse_complement(dna):
""" Computes the reverse complementary sequence of DNA for the specfied DNA
sequence
dna: a DNA sequence represented as a string
returns: the reverse complementary DNA sequence represented as a string
>>> get_reverse_complement("ATGCCCGCTTT")
'AAAGCGGGCAT'
>>> get_reverse_complement("CCGCGTTCA")
'TGAACGCGG'
"""
dna_complement = get_complement(dna)
dna_reverse_complement = dna_complement[::-1] # reverse the complement
return dna_reverse_complement
def rest_of_ORF(dna):
""" Takes a DNA sequence that is assumed to begin with a start
codon and returns the sequence up to but not including the
first in frame stop codon. If there is no in frame stop codon,
returns the whole string.
dna: a DNA sequence
returns: the open reading frame represented as a string
>>> rest_of_ORF("ATGTGAA")
'ATG'
>>> rest_of_ORF("ATGAGATAGG")
'ATGAGA'
"""
i = 0
while i <= len(dna) - 3:
if dna[i:i + 3] == "TAG" or dna[i:i + 3] == "TAA" or dna[i:i + 3] == "TGA":
return dna[0:i]
else:
i = i + 3
return dna
def find_all_ORFs_oneframe(dna):
""" Finds all non-nested open reading frames in the given DNA
sequence and returns them as a list. This function should
only find ORFs that are in the default frame of the sequence
(i.e. they start on indices that are multiples of 3).
By non-nested we mean that if an ORF occurs entirely within
another ORF, it should not be included in the returned list of ORFs.
dna: a DNA sequence
returns: a list of non-nested ORFs
>>> find_all_ORFs_oneframe("ATGCATGAATGTAGATAGATGTGCCC")
['ATGCATGAATGTAGA', 'ATGTGCCC']
"""
final_list = []
i = 0
while i <= len(dna) - 3:
codon = dna[i:i + 3]
if codon == "ATG":
orf = rest_of_ORF(dna[i:])
final_list.append(orf)
i = i + len(orf) + 3
else:
i = i + 3
return final_list
def find_all_ORFs(dna):
""" Finds all non-nested open reading frames in the given DNA sequence in
all 3 possible frames and returns them as a list. By non-nested we
mean that if an ORF occurs entirely within another ORF and they are
both in the same frame, it should not be included in the returned list
of ORFs.
dna: a DNA sequence
returns: a list of non-nested ORFs
>>> find_all_ORFs("ATGCATGAATGTAG")
['ATGCATGAATGTAG', 'ATGAATGTAG', 'ATG']
"""
final_list = []
for i in range(0,3):
orf = find_all_ORFs_oneframe(dna[i:])
final_list.extend(orf)
return final_list
def find_all_ORFs_both_strands(dna):
""" Finds all non-nested open reading frames in the given DNA sequence on both
strands.
dna: a DNA sequence
returns: a list of non-nested ORFs
>>> find_all_ORFs_both_strands("ATGCGAATGTAGCATCAAA")
['ATGCGAATG', 'ATGCTACATTCGCAT']
"""
all_orf_1 = find_all_ORFs(dna)
strand_dna_1 = get_reverse_complement(dna)
all_orf_2 = find_all_ORFs(strand_dna_1)
return list(all_orf_1 + all_orf_2)
##################################################### End of Week1 #####################################################
def longest_ORF(dna):
""" Finds the longest ORF on both strands of the specified DNA and returns it
as a string
>>> longest_ORF("ATGCGAATGTAGCATCAAA")
'ATGCTACATTCGCAT'
"""
longest_orf = find_all_ORFs_both_strands(dna)
a = 0
s = ''
for i in longest_orf:
if len(i) > a:
a = len(i)
s = i
return s
def longest_ORF_noncoding(dna, num_trials):
""" Computes the maximum length of the longest ORF over num_trials shuffles
of the specfied DNA sequence
dna: a DNA sequence
num_trials: the number of random shuffles
returns: the maximum length longest ORF """
s = 0
longest_orf_1 = ""
p = 0
for i in range(0, num_trials):
shuffled_dna = shuffle_string(dna)
longest_orf_1 = longest_ORF(shuffled_dna)
if len(longest_orf_1) > p:
p = len(longest_orf_1)
return p
def coding_strand_to_AA(dna):
""" Computes the Protein encoded by a sequence of DNA. This function
does not check for start and stop codons (it assumes that the input
DNA sequence represents an protein coding region).
dna: a DNA sequence represented as a string
returns: a string containing the sequence of amino acids encoded by the
the input DNA fragment
>>> coding_strand_to_AA("ATGCGA")
'MR'
>>> coding_strand_to_AA("ATGCCCGCTTT")
'MPA'
"""
m = []
s = 0
while s <= len(dna) - 3:
m.append(aa_table[dna[s:s + 3]])
s = s + 3
k = ''
k = k.join(m)
return k
def gene_finder(dna):
""" Returns the amino acid sequences that are likely coded by the specified dna
dna: a DNA sequence
returns: a list of all amino acid sequences coded by the sequence dna.
"""
ac = []
threshold = longest_ORF_noncoding(dna, 1500)
dna_long = find_all_ORFs_both_strands(dna)
for i in dna_long:
if len(i) > threshold:
ac.append(coding_strand_to_AA(i))
return ac
if __name__ == "__main__":
import doctest
print(gene_finder(dna=load_seq("./data/X73525.fa")))
doctest.testmod(verbose=True)