def test_rna_translate_rosalind_data():
print("Positive Test case #1: Rosalind Sample Data")
rosalind_data_file = open("rosalind_data.txt", "r")
rosalind_data_list = rosalind_data_file.readlines()
rosalind_data_file.close()
rosalind_data_list[0] = rosalind_data_list[
0][:-1] # trim off the new line char
print("Result: " +
str(rna_translate(rosalind_data_list[0]) == rosalind_data_list[1]))
print()
def test_rna_translate_no_stop():
print("Negative Test case #1: No stop codon")
rosalind_data_file = open("rosalind_data.txt", "r")
rosalind_data_list = rosalind_data_file.readlines()
rosalind_data_file.close()
rosalind_data_list[0] = rosalind_data_list[
0][:-1] # trim off the new line char
rosalind_data_list[0] = rosalind_data_list[
0][:-3] # remove the stop codon from the end
expected_output = "No valid stop codon found" # returns this error return
print("Result: " +
str(rna_translate(rosalind_data_list[0]) == expected_output))
print()
def test_rna_translate_invalid_codon():
print("Negative Test case #2: Invalid Codon")
print("Note: Should see a warning about an invalid codon")
rosalind_data_file = open("rosalind_data.txt", "r")
rosalind_data_list = rosalind_data_file.readlines()
rosalind_data_file.close()
rosalind_data_list[0] = rosalind_data_list[
0][:-1] # trim off the new line char
rosalind_data_list[0] = "ABC" + rosalind_data_list[
0] # add a nonsense codon to the beginning
# should ignore the invalid codon
output = rna_translate(rosalind_data_list[0])
print("Result: " + str(output == rosalind_data_list[1]))
print()
def translate_RNA_splice(file):
'''
(file) -> str
File contains a dna sequence and introns in FASTA format
Return the protein translation of the dna sequence after introns have been spliced
>>> translate_RNA_splice('splice_example.txt')
MVYIADKQHVASREAYGHMFKVCA*
'''
# convert the FASTA sequences into a single string
# store the single string sequences and their ID in a dictionnary
ID_seq = {}
myfile = open(file, 'r')
for line in myfile:
line = line.rstrip()
if line == '':
continue
elif line.startswith('>'):
ID_seq[line[1:]] = ""
seq_name = line[1:]
else:
ID_seq[seq_name] += line
# make a list with the single string sequences
single_seq = []
for key in ID_seq:
single_seq.append(ID_seq[key])
# make a list with the length of single_seq
seq_length = []
for i in single_seq:
seq_length.append(len(i))
# get the index of the longest single_seq
longest = seq_length.index(max(seq_length))
# add each single_seq to the list of sequences starting with the longest
sequences = []
sequences.append(single_seq[longest])
single_seq.remove(single_seq[longest])
for i in single_seq:
sequences.append(i)
# if the sequence is already a single string and not fasta the vode below is enough
## sequences = []
## for line in myfile:
## line = line.rstrip()
## if not line.startswith('>'):
## sequences.append(line)
# verify that the first sequence in the list is the dna sequence
for i in range(1, len(sequences)):
assert len(sequences[0]) >= len(sequences[i]), 'dna is not the first sequence'
# make a list of tuple that includes the start and end positions of each intron
dna = sequences[0]
intron_positions = []
for i in range(1, len(sequences)):
intron = sequences[i]
intron_start = dna.index(intron)
intron_end = intron_start + len(intron) -1
intron_positions.append((intron_start, intron_end))
# sort the list to get the introns in their order of appearance in dna
intron_positions.sort()
exons = []
# add the first exon to the spliced_dna
exon1 = dna[0:intron_positions[0][0]]
spliced_dna = exon1
# add the other exons using the intron_positions as coordinates
for i in range(1, len(intron_positions)):
exon = dna[intron_positions[i-1][1]+1:intron_positions[i][0]]
spliced_dna += exon
# add the last exon
spliced_dna = spliced_dna + dna[intron_positions[-1][1]+1:]
rna = spliced_dna.upper().replace('T', 'U')
import rna_translate
protein = rna_translate.rna_translate(rna)
return protein