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Graded Homework 3 #1

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56 changes: 36 additions & 20 deletions hw3/gene_finder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,11 @@
from amino_acids import aa, codons
from random import shuffle
from load import load_seq
dna = load_seq("./data/X73525.fa")


def collapse(L):
""" Converts a list of strings to a string by concatenating all elements of the list """
# Try "".join(L) for shorter code
output = ""
for s in L:
output = output + s
Expand All @@ -34,17 +35,16 @@ def coding_strand_to_AA(dna):
for k in range(len(codons[j])):
if dna[3*i:3*i+3] == codons[j][k]:
code += aa[j]
# You can your code more efficient by breaking out of the amino acid search after you've found 1 match
return code

print coding_strand_to_AA("ATGCCCGCTTTT")

def coding_strand_to_AA_unit_tests():
""" Unit tests for the coding_strand_to_AA function """
print "input: " + "ATGCCCGCTTTT"
print "expected output: " + "MPAF"
print "actual output: " + coding_strand_to_AA("ATGCCCGCTTTT")

coding_strand_to_AA_unit_tests()

def get_reverse_complement(dna):
""" Computes the reverse complementary sequence of DNA for the specfied DNA
Expand All @@ -65,15 +65,13 @@ def get_reverse_complement(dna):
complement+= 'C'

return complement[::-1]
print get_reverse_complement("ATGCCCGCTTT")

def get_reverse_complement_unit_tests():
""" Unit tests for the get_complement function """
print "input: " + "ATGCCCGCTTAT"
print "expected output: " + "ATAAGCGGGCAT"
print "actual output: " + get_reverse_complement("ATGCCCGCTTAT")

get_reverse_complement_unit_tests()

def rest_of_ORF(dna):
""" Takes a DNA sequence that is assumed to begin with a start codon and returns
Expand All @@ -90,15 +88,13 @@ def rest_of_ORF(dna):
codelove+=dna[3*i:3*i+3]
return codelove

print rest_of_ORF("ATGAGATAGG")

def rest_of_ORF_unit_tests():
""" Unit tests for the rest_of_ORF function """
print "input: " + "ATGAGATAGGG"
print "expected output: " + "ATGAGA"
print "actual output: " + rest_of_ORF("ATGAGATAGGG")

rest_of_ORF_unit_tests()

def find_all_ORFs_oneframe(dna):
""" Finds all non-nested open reading frames in the given DNA sequence and returns
Expand All @@ -121,7 +117,6 @@ def find_all_ORFs_oneframe(dna):
i+=1
return codelove

print find_all_ORFs_oneframe("ATGCATGAATGTAGATAGATGTGCCC")

def find_all_ORFs_oneframe_unit_tests():
""" Unit tests for the find_all_ORFs_oneframe function """
Expand All @@ -130,7 +125,6 @@ def find_all_ORFs_oneframe_unit_tests():
print "expected output: " + "['ATGCATGAATGTAGA', 'ATGTGCACC']"
print "actual output: " + str(find_all_ORFs_oneframe("ATGCATGAATGTAGATAGATGTGCACC"))

find_all_ORFs_oneframe_unit_tests()

def find_all_ORFs(dna):
""" Finds all non-nested open reading frames in the given DNA sequence in all 3
Expand All @@ -146,15 +140,13 @@ def find_all_ORFs(dna):
new.extend(find_all_ORFs_oneframe(dna[i:]))
return new

print find_all_ORFs("ATGCATGAATGTAG")

def find_all_ORFs_unit_tests():
""" Unit tests for the find_all_ORFs function """
print "input: " + "ATGCATGAATGTAGATAGATGTGCCC"
print "expected output: " + "['ATGCATGAATGT', 'ATGAATGTA', 'ATG']"
print "actual output: " + str(find_all_ORFs("ATGCATGAATGTAG"))

find_all_ORFs_unit_tests()

def find_all_ORFs_both_strands(dna):
""" Finds all non-nested open reading frames in the given DNA sequence on both
Expand All @@ -168,7 +160,6 @@ def find_all_ORFs_both_strands(dna):

return loco1

print find_all_ORFs_both_strands("ATGCGAATGTAGCATCAAA")

def find_all_ORFs_both_strands_unit_tests():
""" Unit tests for the find_all_ORFs_both_strands function """
Expand All @@ -177,26 +168,23 @@ def find_all_ORFs_both_strands_unit_tests():
print "expected output: " + "['ATGCGAATG', 'ATGCTACATTCGCAT']"
print "actual output: " + str(find_all_ORFs_both_strands("ATGCGAATGTAGCATCAAAA"))

find_all_ORFs_both_strands_unit_tests()

def longest_ORF(dna):
""" Finds the longest ORF on both strands of the specified DNA and returns it
as a string"""
if find_all_ORFs_both_strands(dna)==[]:
return ''
else:
else: # is there a point to assigning a variable "a"here? why not use return the expression?
a=max(find_all_ORFs_both_strands(dna),key=len)
return a

print longest_ORF("ATGCGAATGTAGCATTCAAA")

def longest_ORF_unit_tests():
""" Unit tests for the longest_ORF function """
print "input: " + "ATGCGAATGTAGCATCAAA"
print "expected output: " + "ATGCTACATTCGCAT"
print "actual output: " + str(longest_ORF("ATGCGAATGTAGCATTCAAA"))

longest_ORF_unit_tests()

def longest_ORF_noncoding(dna, num_trials):
""" Computes the maximum length of the longest ORF over num_trials shuffles
Expand All @@ -214,7 +202,6 @@ def longest_ORF_noncoding(dna, num_trials):
lorg = f
return len(lorg)

print longest_ORF_noncoding(dna,1500)

def gene_finder(dna, threshold):
""" Returns the amino acid sequences coded by all genes that have an ORF
Expand All @@ -232,9 +219,38 @@ def gene_finder(dna, threshold):
while r<len(loco2):
if len(loco2[r])>threshold:
p.append(coding_strand_to_AA(loco2[r]))
r+=1
r+=1 # If you're going to be r += 1 no matter what happens, take them out of the if else statements
else:
r+=1
""" Edit - without while loop
p = []
for r in loco2:
if len(r) < threshold:
p.append(coding_strand_to_AA(r))
return p

print gene_finder(dna, 666)
"""

return p

if __name__ == "__main__":
# It's great that you're running tests on all your functions, but please put them in an
# if __name__ == "__main__" statement to prevent side-effect printing to occur when we
# import your module.
# Also, try doing stress tests with your tests next time. (extreme arguments - empty string, wrong # of strings, wrong characters, etc...)
dna = load_seq("./data/X73525.fa")
print coding_strand_to_AA_unit_tests
coding_strand_to_AA_unit_tests()
print get_reverse_complement("ATGCCCGCTTT")
get_reverse_complement_unit_tests()
print rest_of_ORF("ATGAGATAGG")
rest_of_ORF_unit_tests()
print find_all_ORFs_oneframe("ATGCATGAATGTAGATAGATGTGCCC")
find_all_ORFs_oneframe_unit_tests()
print find_all_ORFs("ATGCATGAATGTAG")
find_all_ORFs_unit_tests()
print find_all_ORFs_both_strands("ATGCGAATGTAGCATCAAA")
find_all_ORFs_both_strands_unit_tests()
print longest_ORF("ATGCGAATGTAGCATTCAAA")
longest_ORF_unit_tests()
print longest_ORF_noncoding(dna,1500)
print gene_finder(dna, 666)