I want to identify the keys from a dictionary (strings) in a DNA sequence(string or fasta).
How can I find the keys in the sequence and get? I've tried something like this:
def identification(ren, S):
patternkeys = []
for key in ren:
if S in key:
patternkeys.append(key)
return patternKeys
patterns = []
patterns = identification(ren, S)
print patterns
#..............
ren is the dictionary and S the sequence
I need to get keys and values FOUND in the sequence.
Thanks
•
written
by
albamaria.muniesa •
It's not necessary to get all the keys and values, only those found in the sequence.
Not sure if this is what you want, but this should do the trick:
patternkeys = [x for x in ren.keys() if ren[x] in S]
In any case, for this type of programming questions you should better ask in stackoverflow.
•
written
by
Giovanni M Dall'Olio
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not terribly efficient, but you could modify the line
"if S in key" to use a regular expression that identifies key in S. See e.g. http://stackoverflow.com/questions/7345252/python-regex-match-words-in-string-and-get-count