def test_partition():
assert functional.partition(lambda e: e % 3 == 0,
functional.range(1, 11)) == \
[ [ 3, 6, 9 ], [ 1, 2, 4, 5, 7, 8, 10 ] ]
assert functional.partition(lambda e: e % 3 != 0,
functional.range(1, 11)) == \
[ [ 1, 2, 4, 5, 7, 8, 10 ], [ 3, 6, 9 ] ]
assert functional.partition(lambda e: e == 0,
functional.range(1, 11)) == \
[ [], [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 ] ]
assert functional.partition(lambda e: len(e) > 1,
[ [ 1 ], [ 1, 2 ], [ 1, 2, 3 ] ]) == \
[ [ [ 1, 2 ], [ 1, 2, 3 ] ], [ [ 1 ] ] ]
from sequence import rev_complement
from fastamasta import FastaReader
from functional import partition
if __name__ == "__main__":
seq = [i for i in FastaReader("data/44.fas")][0][1]
rev_palindromes = []
for i in range(4, 13):
parts = [''.join(x) for x in partition(seq, i, list)]
for j in range(len(parts)):
if parts[j] == rev_complement(parts[j]):
rev_palindromes.append((j + 1, i))
for tup in rev_palindromes:
print tup[0], tup[1]
from fastamasta import FastaReader
from functional import partition
if __name__ == "__main__":
data = []
for datum in FastaReader("data/21.fas"):
data.append(datum[1])
shortest = ' ' * 1001
for i in data:
if len(i) < len(shortest):
shortest = i
data.remove(shortest)
print data
for i in range(2, len(shortest) + 1)[::-1]:
parts = [i for i in partition(shortest, i, str)]
for part in parts:
in_all = True
for datum in data:
if part not in datum:
in_all = False
break
if in_all:
print part
from functional import partition, frequencies
from fastamasta import FastaReader
def alphabet(order, length, string='', arr=None):
if arr is None:
arr=[]
if length == 0:
arr.append(string)
else:
for char in order:
alphabet(order, length-1, string + char, arr)
return arr
if __name__ == "__main__":
with open("data/13.dat", 'r') as data_file:
reader = FastaReader('data/14.dat')
data = reader.readnext()
order, size = ['A', 'C', 'G', 'T'], 4
alph = alphabet(order, size)
fourmer_count = frequencies(partition(data[1], size, str))
output = ''
for word in alph:
output += str(fourmer_count.get(word, 0)) + ' '
print output
from functional import partition, frequencies
import operator
if __name__ == '__main__':
with open('data/4.ini', 'r') as data_file:
data = data_file.readline()
k, L, t = data_file.readline().split(' ')
k, L, t = int(k), int(L), int(t)
kmers = [
i for i in partition(list(data), k,
lambda x: reduce(operator.add, x))
]
kmers_count = frequencies(kmers)
viable_kmers = set(key for key, val in kmers_count.items()
if (val >= t))
viable_kmer_idxs = {}
for i in range(len(kmers)):
if kmers[i] in viable_kmers:
temp_arr = viable_kmer_idxs.get(kmers[i], [])
temp_arr.append(i)
viable_kmer_idxs[kmers[i]] = temp_arr
L_t_clumps = set()
for (key, val) in viable_kmer_idxs.items():
for i in range(len(val) - (t - 1)):
if ((val[i + t - 1] - val[i]) <= (L - t)):
L_t_clumps.add(key)
print ' '.join(map(str, L_t_clumps))