Commit e7ea101e authored by Bertrand  NÉRON's avatar Bertrand NÉRON
Browse files

simplify exercise on seraching restriction enzyme site in dna

parent 8f8e84a4
......@@ -203,62 +203,35 @@ and the 2 dna fragments: ::
dna_1 = dna_1.replace('\n', '')
dans_2 = dna_2.replace('\n', '')
algorithm 1 ::
enzymes = [ecor1, ecor5, bamh1, hind3, taq1, not1, sau3a1, hae3, sma1]
digest_1 = []
for enz in enzymes:
pos = dna_1.find(enz.sequence)
if pos != -1:
if enz.sequence in dna_1:
digest_1.append(enz)
with this first algorithm we find if an enzyme cut the dna but we cannot find all cuts in the dna for an enzyme.
If we find a cutting site, we must search again starting at the first nucleotid after the begining of the match
until the end of the the dna, for this we use the start parameter of the find function, and so on.
As we don't know how many loop we need to scan the dna until the end we use a ``while`` loop testing for the presence of a cutting site.::
algorithm 2 we can determine the position of the site ::
enzymes = [ecor1, ecor5, bamh1, hind3, taq1, not1, sau3a1, hae3, sma1]
digest_1 = []
for enz in enzymes:
pos = dna_1.find(enz.sequence)
while pos != -1:
if pos != -1:
digest_1.append(enz)
pos = dna_1.find(enz.sequence, pos + 1)
digest_2 = []
for enz in enzymes:
pos = dna_2.find(enz.sequence)
while pos != -1:
digest_2.append(enz)
pos = dna_2.find(enz.sequence, pos + 1)
cut_dna_1 = set(digest_1)
cut_dna_2 = set(digest_2)
cut_dna_1_not_dna_2 = cut_dna_1 - cut_dna_2
If we want also the position, for instance to compute the fragments of dna. ::
with these algorithms we find if an enzyme cut the dna but we cannot find all cuts in the dna for an enzyme. ::
enzymes = [ecor1, ecor5, bamh1, hind3, taq1, not1, sau3a1, hae3, sma1]
digest_1 = []
for enz in enzymes:
pos = dna_1.find(enz.sequence)
while pos != -1:
digest_1.append((enz, pos))
pos = dna_1.find(enz.sequence, pos + 1)
from operator import itemgetter
digest_1.sort(key=itemgetter(1))
[(e.name, d) for e, d in digest_1]
digest_2 = []
for enz in enzymes:
pos = dna_2.find(enz.sequence)
while pos != -1:
digest_2.append((enz, pos))
pos = dna_2.find(enz.sequence, pos + 1)
cut_dna_1 = set([e.name for e in digest_1])
cut_dna_2 = set([e.name for e in digest_2])
cut_dna_1_not_dna_2 = cut_dna_1 - cut_dna_2
print enz.name, dna_1.count(enz.sequence)
the latter algorithm display the number of occurence of each enzyme, But we cannot determine the position of every sites.
We will see howt to do this later.
Exercise
......
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