Forked from Neemox/Generating nucleotide degeneracy permutations
Created
February 17, 2015 21:18
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import re | |
import csv | |
re_degenerates = re.compile(r"[wsmkrybdhvn]") | |
def get_patterns(filename): | |
with open(filename) as f: | |
#lines = f.readlines()[2:] # the first two lines aren't data | |
lines = f.readlines() | |
for record in csv.reader(lines): | |
index = record[0] # the first column is the pattern id | |
pattern = record[1] #this *should look at the second column in the CSV | |
# pattern = "".join(record[1:]) # the rest of the columns are nucleotides (This line was for separated nucleotides uin the CSV) | |
yield index, pattern | |
def has_degenerate(pattern): | |
return re_degenerates.search(pattern) is not None | |
def get_permutations(pattern): | |
""" Return all of the possible interpretation/permutations of pattern | |
pattern is a string that matches /[actgwsmkrybdhvn]+/ | |
Usage: | |
>>> tuple(get_permutations("acww")) | |
('acaa', 'acat', 'acta', 'actt') | |
""" | |
_degeneracy = { | |
"w": ("a", "t"), | |
"s": ("c", "g"), | |
"m": ("a", "c"), | |
"k": ("g", "t"), | |
"r": ("a", "g"), | |
"y": ("c", "t"), | |
"b": ("c", "g", "t"), | |
"d": ("a", "g", "t"), | |
"h": ("a", "c", "t"), | |
"v": ("a", "c", "g"), | |
"n": ("a", "c", "g", "t"), | |
} | |
if has_degenerate(pattern): | |
for nuc in pattern: | |
if nuc in _degeneracy: | |
for resolved_nuc in _degeneracy[nuc]: | |
new_pattern = pattern.replace(nuc, resolved_nuc, 1) | |
yield from get_permutations(new_pattern) | |
break | |
else: | |
yield pattern | |
def find_sequence(sequence, degenerate_pattern): | |
""" Return true if sequence is in any of the permutations of degenerate_pattern. | |
sequence must consist only of real base pairs. (it must match /[actg]+/) | |
""" | |
re_sequence = re.compile(sequence) | |
for permutation in get_permutations(degenerate_pattern): | |
match = re_sequence.search(permutation) | |
if match: | |
print("Matched sequence '{0}' in permutation '{1}' at position {2}".format(sequence, swaprange(permutation, *match.span()), match.span())) | |
return False | |
def main(sequence): | |
for id, pattern in get_patterns("data.csv"): | |
print("Permuting pattern {0}".format(id)) | |
if not find_sequence(sequence, pattern): | |
print("Found no matches") | |
print() | |
def swaprange(s, left, right): | |
return s[:left] + s[left:right].swapcase() + s[right:] |
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