>Rosalind_9712
GTGCCGCCTCAGACTTACAGGCACTGCCCGCGGCTCATCAGAGGGGTTGTTGCTAACGAT
AGAAGAATTACCTGGCTTGCCACGCGCCTGAGAACGGAAACCATTATATGCTGAGCACCC
GAGCTGTAAGGTTTCGCACTGCCAAACGCGAGGCGGCAAGGGAGGGTCTGTATCAGGGAC
AGAATAATCAAGGCGATCCGTCAAGACCGCCGCGTGAAGCGAGATCACTTCTGTTAGGTC
GAGGTCGTAACGCCTGGCTATGCTTATCGAGCCAAAAGCATCTTATAAGCAAGACACCTC
GTAATTCAAGCGCATGTCACTGCTCAATCGTGAGTTCATCTGTGAGAACGTTTTCGCCAA
CAGTGACTCTGAGGCCTAACGCCTCAATAAGTGAGAAGGTGACCCCGATACGACCCACCG
AAGTTAACATCAATAAGTATGTATTCATGAACACAAACTTCTCCTTGGTACGGCCATAGG
TACAATGGAAAGTAGTGATATTGGGATGGTGACCTCGGCGCCTACCCCTAGCCAGCCGGT
CATAAATTTTACAACCGCGCTACAGAGCCAGCGCTTGGGTGCTTCCCGTGCCTTTCAATT
ACGCGATTCATCTGGTCATATGGACGTATATTGGAGTTATGGGCAATATAGTTGTTCGCT
CTAGCCCGAAGATAAACACCACTCTTAAGTCATCGCAAACTACCTGACAGGGAGACCTTC
CCTCCACATCAGTCTAATGCATCGCAGCAACACAACCCGCCCGCGCTTATCTGGGAAATG
CTCGAAATGGGGGCATCTTTGAGCTC
>Rosalind_6280
AAGTAGATTACCCGTTCT
'''
seqs = read_fasta(data)
ref = str(seqs[0].sequence)
substring = seqs[1].sequence
indexes = list()
i = 0
for char in substring:
i = ref.find(char, i) +1
if (i >= 0):
indexes.append(i)
for x in indexes:
print x,
import numpy as np
from fasta.Fasta import read_fasta
# hetland.org/coding/python/levenshtein.py
def levenshtein(a,b):
"Calculates the Levenshtein distance between a and b."
n, m = len(a), len(b)
if n > m:
# Make sure n <= m, to use O(min(n,m)) space
a,b = b,a
n,m = m,n
current = range(n+1)
for i in range(1,m+1):
previous, current = current, [i]+[0]*n
for j in range(1,n+1):
add, delete = previous[j]+1, current[j-1]+1
change = previous[j-1]
if a[j-1] != b[i-1]:
change = change + 1
current[j] = min(add, delete, change)
return current[n]
if __name__ == '__main__':
data = open("rosalind_edit_1_dataset.txt", 'r').read()
fasta = read_fasta(data)
print levenshtein(fasta[0].sequence, fasta[1].sequence)
#print levenshtein('PLEASANTLY', 'MEANLY')
P19835_BAL_HUMAN
O13188
P02760_HC_HUMAN
Q4FZD7
Q00001_RHGA_ASPAC
Q47A87
Q8R1Y2
A6NM15
P22457_FA7_BOVIN
P03415_VME1_CVMA5
P11171_41_HUMAN
'''
for x in filter(None, data.split('\n')):
url = 'http://www.uniprot.org/uniprot/' + x + '.fasta'
fasta_content = urlopen(url).read()
seq = read_fasta(fasta_content)
indexes = list()
s = seq[0].sequence
matches = filter(None, list(re.finditer(le_regex_1, s)))
if (len(matches) > 0):
for m in matches:
if m not in indexes:
indexes.append( m.start()+1)
matches = filter(None, list(re.finditer(le_regex_2, s)))
if (len(matches) > 0):
for m in matches:
if m not in indexes:
indexes.append( m.start()+1)
if (len(indexes) > 0):
def stacksize(since=0.0):
'''Return stack size in bytes.
'''
return _VmB('VmStk:') - since
if __name__ == '__main__':
start_time = time.time()
data = '''
>Rosalind_92
AUGCUUC
'''
m0 = memory()
# le sequence
sequence = read_fasta(data)[0].sequence
au_count1, au_count2 = sorted([sequence.count('A'), sequence.count('U')])
cg_count1, cg_count2 = sorted([sequence.count('C'), sequence.count('G')])
matchings = 1
for i in range(au_count1):
matchings *= (au_count2 - i)
for j in range(cg_count1):
matchings *= (cg_count2 - j)
print matchings
m1 = memory(m0)
print m1
