def read_words(filename):
"""
Load word list from the file named filename.
Returns a list of strings.
"""
# load assets
word_file = urllib2.urlopen(filename)
# read in files as string
words = word_file.read()
# template lines and solution lines list of line string
word_list = words.split('\n')
print "Loaded a dictionary with", len(word_list), "words"
return word_list
human = read_protein(HUMAN_EYELESS_URL)
fruitfly = read_protein(FRUITFLY_EYELESS_URL)
s_m = read_scoring_matrix(PAM50_URL)
a_m = student.compute_alignment_matrix(human, fruitfly, s_m, False)
alignment = student.compute_local_alignment(human, fruitfly, s_m, a_m)
print alignment[0]
print "Human :", alignment[1]
print "Fruitfly:", alignment[2]
return protein_seq
def read_words(filename):
"""
Load word list from the file named filename.
Returns a list of strings.
"""
# load assets
word_file = urllib2.urlopen(filename)
# read in files as string
words = word_file.read()
# template lines and solution lines list of line string
word_list = words.split('\n')
print "Loaded a dictionary with", len(word_list), "words"
return word_list
human = read_protein(HUMAN_EYELESS_URL)
fruitfly = read_protein(FRUITFLY_EYELESS_URL)
s_m = read_scoring_matrix(PAM50_URL)
a_m = student.compute_alignment_matrix(human, fruitfly, s_m, False)
alignment = student.compute_local_alignment(human, fruitfly, s_m, a_m)
print alignment[0]
print "Human :", alignment[1]
print "Fruitfly:", alignment[2]
word_file = urllib2.urlopen(filename)
# read in files as string
words = word_file.read()
# template lines and solution lines list of line string
word_list = words.split('\n')
print "Loaded a dictionary with", len(word_list), "words"
return word_list
human = "HSGVNQLGGVFVNGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATPEVVSKIAQYKRECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLASEKQQ"
fruitfly = "HSGVNQLGGVFVGGRPLPDSTRQKIVELAHSGARPCDISRILQVSNGCVSKILGRYYETGSIRPRAIGGSKPRVATAEVVSKISQYKRECPSIFAWEIRDRLLQENVCTNDNIPSVSSINRVLRNLAAQKEQQ"
s_m = read_scoring_matrix(PAM50_URL)
consensus = read_protein(CONSENSUS_PAX_URL)
a_m = student.compute_alignment_matrix(human, consensus, s_m, True)
alignment = student.compute_global_alignment(human, consensus, s_m, a_m)
print "Score :", alignment[0]
print "Human :", alignment[1]
print "Consensus:", alignment[2]
percent = 0
for i in xrange(len(alignment[1])):
if alignment[1][i] == alignment[2][i]:
percent += 1
print "Percent :", 100.0 * percent / len(alignment[1])
a_m = student.compute_alignment_matrix(fruitfly, consensus, s_m, True)
alignment = student.compute_global_alignment(fruitfly, consensus, s_m, a_m)
print "Score :", alignment[0]
print "Fruitfly :", alignment[1]
print "Consensus:", alignment[2]
