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Homework 3 has been graded #1

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41 changes: 26 additions & 15 deletions hw3/gene_finder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ def find_Amino_Acid(currentCodon):

def collapse(L):
""" Converts a list of strings to a string by concatenating all elements of the list """

#Try "".join(L)
output = ""
for s in L:
output = output + s
Expand Down Expand Up @@ -73,11 +73,11 @@ def get_reverse_complement(dna):
dna: a DNA sequence represented as a string
returns: the reverse complementary DNA sequence represented as a string
"""

# YOUR IMPLEMENTATION HERE
#This isn't quite right, conceptually.
#Reverse_complement is both the complement and the reverse of the string itself

newDna = ""
for i in range (len(dna)):
for i in range (len(dna)): # if this was changed to: for i in range(len(dna),0,-1): it might work.
if (dna[i]=='A'):
newDna += 'T'

Expand Down Expand Up @@ -107,9 +107,14 @@ def rest_of_ORF(dna):
dna: a DNA sequence
returns: the open reading frame represented as a string
"""
# UHOH, your loop is too long! It's going beyond the string. Granted you got lucky and its not breaking, but
# as it is now, you will be trying to access indices of the list beyond the length of the list
# this is generally bad coding style.
#either make sure you only loop through range(len(dna)/3) or loop through range(0,len(dna),3)
dnaSequence = ""
for i in range (len(dna)):
nextCodon = dna[3*i:3*i+3]
print len(dna), 3*i+3
if (stopCodon(nextCodon)):
break
dnaSequence = dnaSequence + nextCodon
Expand Down Expand Up @@ -145,6 +150,7 @@ def find_all_ORFs_oneframe(dna):
dna: a DNA sequence
returns: a list of non-nested ORFs
"""

ORFs = []
i = 0
while (i < len(dna)):
Expand Down Expand Up @@ -201,9 +207,16 @@ def find_all_ORFs(dna):
dna: a DNA sequence
returns: a list of non-nested ORFs
"""

# When you have repetition like this, it generally means you can throw it in a for loop
# for i in range(3):
# frameshift = dna[i:]
# shifts = find_all_ORFs_oneframe(frameshift)
# for shift in shifts:
# all_ORFS.append(shift)
# return all_ORFs

frame0Shift = dna
frame1Shift = dna[1:len(dna)]
frame1Shift = dna[1:len(dna)] #if you want to include to the end, simply doing dna[1:] will work
frame2Shift = dna[2:len(dna)]

list0Shift = find_all_ORFs_oneframe(frame0Shift)
Expand Down Expand Up @@ -335,14 +348,12 @@ def gene_finder(dna, threshold):
list_Of_ORFs = find_all_ORFs_both_strands(dna)
list_Of_Genes = []
aminoAcidSequences = []
for i in range(len(list_Of_ORFs)):
currentLength = len(list_Of_ORFs[i])

if(currentLength >= threshold):
list_Of_Genes.append(list_Of_ORFs[i])
for ORF in list_Of_ORFs:
if(len(ORF >= threshold):
list_Of_Genes.append(ORF)

for i in range (len(list_Of_Genes)):
currentDna = list_Of_Genes[i]
for gene in list_Of_Genes:
currentDna = gene
aminoAcid = coding_strand_to_AA(currentDna)
aminoAcidSequences.append(aminoAcid)

Expand All @@ -356,4 +367,4 @@ def gene_finder(dna, threshold):
print threshold
aminoAcids = gene_finder(dna, threshold)
for i in range(len(aminoAcids)):
print aminoAcids[i]
print aminoAcids[i]