From e7ea101ef897ef3316944932a27779bcefe95bae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= <bneron@pasteur.fr>
Date: Tue, 12 Aug 2014 23:56:53 +0200
Subject: [PATCH] simplify exercise on seraching restriction enzyme site in
dna
---
source/Collection_Data_Types.rst | 61 +++++++++-----------------------
1 file changed, 17 insertions(+), 44 deletions(-)
diff --git a/source/Collection_Data_Types.rst b/source/Collection_Data_Types.rst
index 7a4e7b7..2584f1c 100644
--- a/source/Collection_Data_Types.rst
+++ b/source/Collection_Data_Types.rst
@@ -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
--
GitLab