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hub-courses
python_one_week_4_biologists_solutions
Commits
ef3842e6
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Commit
ef3842e6
authored
Mar 11, 2019
by
Bertrand NÉRON
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remove python2 specific code
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#10138
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source/Collection_Data_Types.rst
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ef3842e6
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@@ -110,19 +110,16 @@ wihout using python shell, what is the results of the following statements:
x[3] = -4 # what is the value of x now ?
y = sum(x)/len(x) #what is the value of y ? why ?
y = 0
y = 0.5
.. warning::
because sum(x) is an integer, len(x) is also an integer so in python2.x the result is an integer,
all the digits after the periods are discarded.
In python3 we will obtain the expected result (see :ref:``)
Exercise
--------
In python2 the result is ::
y = 0
How to compute safely the average of a list? ::
because sum(x) is an integer, len(x) is also an integer so in python2.x the result is an integer,
all the digits after the periods are discarded.
float(sum(l)) / float(len(l))
Exercise
--------
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@@ -206,9 +203,9 @@ first implementation:
second implementation:
""""""""""""""""""""""
Mathematically speaking the generation of all codons can be the cartesi
ens
product
Mathematically speaking the generation of all codons can be the cartesi
an
product
between 3 vectors 'acgt'.
In python there is a function to do that in ``itertools module``: `https://docs.python.org/
2
/library/itertools.html#itertools.product <product>`_
In python there is a function to do that in ``itertools module``: `https://docs.python.org/
3
/library/itertools.html#itertools.product <product>`_
.. literalinclude:: _static/code/codons_itertools.py
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@@ -274,7 +271,7 @@ So we can use the specifycity of set ::
Exercise
--------
We need to compute the occurence of all kmers of a given leng
h
t present in a sequence.
We need to compute the occur
r
ence of all kmers of a given lengt
h
present in a sequence.
Below we propose 2 algorithms.
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@@ -378,8 +375,8 @@ bonus:
Print the kmers by ordered by occurences.
| see `https://docs.python.org/
2
/library/stdtypes.html#mutable-sequence-types <sort>`_
| see `https://docs.python.org/
2
/library/operator.html#operator.itemgetter <operator.itemgetter>`_
| see `https://docs.python.org/
3
/library/stdtypes.html#mutable-sequence-types <sort>`_
| see `https://docs.python.org/
3
/library/operator.html#operator.itemgetter <operator.itemgetter>`_
.. literalinclude:: _static/code/kmer_2.py
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@@ -475,7 +472,7 @@ Exercise
let the following enzymes collection: ::
import collections
RestrictEnzyme = collections.namedtuple("RestrictEnzyme", "name
comment
sequence
cut
end")
RestrictEnzyme = collections.namedtuple("RestrictEnzyme",
(
"name
", "
comment
", "
sequence
", "cut", "
end")
)
ecor1 = RestrictEnzyme("EcoRI", "Ecoli restriction enzime I", "gaattc", 1, "sticky")
ecor5 = RestrictEnzyme("EcoRV", "Ecoli restriction enzime V", "gatatc", 3, "blunt")
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@@ -504,7 +501,7 @@ and the 2 dna fragments: ::
#. Write a function *seq_one_line* which take a multi lines sequence and return a sequence in one line.
#. Write a function *enz_filter* which take a sequence and a list of enzymes and return a new list containing
the enzymes which
ar
e a binding site in the sequence
the enzymes which
hav
e a binding site in the sequence
#. use the functions above to compute the enzymes which cut the dna_1
apply the same functions to compute the enzymes which cut the dna_2
compute the difference between the enzymes which cut the dna_1 and enzymes which cut the dna_2
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@@ -532,7 +529,7 @@ with this algorithm we find if an enzyme cut the dna but we cannot find all cuts
for enz in enzymes:
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.
the latter algorithm display the number of occur
r
ence of each enzyme, But we cannot determine the position of every sites.
We will see how to do this later.
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