.. _Data_Types: ********** Data Types ********** Exercices ========= Exercise -------- Assume that we execute the following assignment statements: :: width = 17 height = 12.0 delimiter ='.' For each of the following expressions, write the value of the expression and the type (of the value of the expression) and explain. #. width / 2 #. width / 2.0 #. height / 3 #. 1 + 2 * 5 Use the Python interpreter to check your answers. :: >>> width = 17 >>> height = 12.0 >>> delimiter ='.' >>> >>> width / 2 8 >>> # both operands are integer so python done an euclidian division and threw out the remainder >>> width / 2.0 8.5 >>> height / 3 4.0 >>> # one of the operand is a float (2.0 or height) then python pyhton perform afloat division but keep in mind that float numbers are aproximation. >>> # if you need precision you need to use Decimal. But operations on Decimal are slow and float offer quite enought precision >>> # so we use decimal only if wee need great precision >>> # Euclidian division >>> 2 / 3 0 >>> # float division >>> float(2)/float(3) 0.6666666666666666 >>> # decimal division >>> from decimal import Decimal >>> a = Decimal(2) >>> b = Decimal(3) >>> a / b Decimal('0.6666666666666666666666666667') >>> 1 + 2 * 5 11 Exercise -------- Write a function which take a radius as input and return the volume of a sphere: The volume of a sphere with radius r is 4/3 πr\ :sup:`3`. What is the volume of a sphere with radius 5? **Hint**: π is in math module, so to access it you need to import the math module Place the ``import`` statement at the top fo your file. after that, you can use ``math.pi`` everywhere in the file like this:: >>> import math >>> >>> #do what you need to do >>> math.pi #use math.pi **Hint**: the volume of a spher with radius 5 is **not** 392.7 ! .. literalinclude:: _static/code/vol_of_sphere.py :linenos: :language: python :: python -i volume_of_sphere.py >>> vol_of_sphere(5) 523.5987755982989 :download:`vol_of_sphere.py <_static/code/vol_of_sphere.py>` . Exercise -------- Draw what happen in memory when the following statements are executed: :: i = 12 i += 2 .. figure:: _static/figs/augmented_assignment_int.png :width: 400px :alt: set :figclass: align-center :: >>> i = 12 >>> id(i) 33157200 >>> i += 2 >>> id(i) 33157152 and :: s = 'gaa' s = s + 'ttc' .. figure:: _static/figs/augmented_assignment_string.png :width: 400px :alt: set :figclass: align-center :: >>> s = 'gaa' >>> id(s) 139950507582368 >>> s = s+ 'ttc' >>> s 'gaattc' >>> id(s) 139950571818896 when an augmented assignment operator is used on an immutable object is that #. the operation is performed, #. and an object holding the result is created #. and then the target object reference is re-bound to refer to the result object rather than the object it referred to before. So, in the preceding case when the statement ``i += 2`` is encountered, Python computes 1 + 2 , stores the result in a new int object, and then rebinds ``i`` to refer to this new int . And if the original object a was referring to has no more object references referring to it, it will be scheduled for garbage collection. The same mechanism is done with all immutable object included strings. Exercise -------- how to obtain a new sequence which is the 10 times repetition of the this motif : "AGGTCGACCAGATTANTCCG":: >>> s = "AGGTCGACCAGATTANTCCG" >>> s10 = s * 10 Exercise -------- create a representation in fasta format of following sequence : .. note:: A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (optional). There should be no space between the ">" and the first letter of the identifier. The sequence ends if another line starting with a ">" appears; this indicates the start of another sequence. :: id = "sp|P60568|IL2_HUMAN" comment = "Interleukin-2 OS=Homo sapiens GN=IL2 PE=1 SV=1" sequence = """MYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRML TFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSE TTFMCEYADETATIVEFLNRWITFCQSIISTLT""" >>> s = id + comment + '\n' + sequence or >>> s = "{id} {comment} \n{sequence}".format(id= id, comment = comment, sequence = sequence) Exercise -------- For the following exercise use the python file :download:`sv40 in fasta <_static/code/sv40.py>` which is a python file with the sequence of sv40 in fasta format already embeded, and use python -i sv40.py to work. how long is the sv40 in bp? Hint : the fasta header is 61bp long. (http://www.ncbi.nlm.nih.gov/nuccore/J02400.1) pseudocode write a function ``fasta_to_one_line`` that return a sequence as a string without header or any non sequence characters pseudocode: | *fasta_to_one_line(seq)* | *header_end_at <- find the first return line character* | *raw_seq <- remove header from sequence* | *raw_seq <- remove non sequence chars* | *return raw_seq* .. literalinclude:: _static/code/fasta_to_one_line.py :linenos: :language: python :download:`fasta_to_one_line.py <_static/code/fasta_to_one_line.py>` . :: python >>> import sv40 >>> import fasta_to_one_line >>> >>> sv40seq = fasta_to_one_line(sv40) >>> print len(sv40_sequence) 5243 Is that the following enzymes: * BamHI (ggatcc), * EcorI (gaattc), * HindIII (aagctt), * SmaI (cccggg) have recogition sites in sv40 (just answer by True or False)? :: >>> "ggatcc".upper() in sv40_sequence True >>> "gaattc".upper() in sv40_sequence True >>> "aagctt".upper() in sv40_sequence True >>> "cccggg".upper() in sv40_sequence False for the enzymes which have a recognition site can you give their positions? :: >>> sv40_sequence = sv40_sequence.lower() >>> sv40_sequence.find("ggatcc") 2532 >>> # remind the string are numbered from 0 >>> 2532 + 1 = 2533 >>> # the recognition motif of BamHI start at 2533 >>> sv40_sequence.find("gaattc") 1781 >>> # EcorI -> 1782 >>> sv40_sequence.find("aagctt") 1045 >>> # HindIII -> 1046 is there only one site in sv40 per enzyme? The ``find`` method give the index of the first occurence or -1 if the substring is not found. So we can not determine the occurence of a site only with the find method. We will see how to do that when we learn looping and conditions. Exercise -------- We want to perform a PCR on sv40, can you give the length and the sequence of the amplicon? Write a function which have 3 parameters ``sequence``, ``primer_1`` and ``primer_2`` * *We consider only the cases where primer_1 and primer_2 are present in sequence* * *to simplify the exercise, the 2 primers can be read directly in the sv40 sequence.* test you algorithm with the following primers | primer_1 : 5' CGGGACTATGGTTGCTGACT 3' | primre_2 : 5' TCTTTCCGCCTCAGAAGGTA 3' Write the pseudocode before to implement it. | *function amplicon_len(sequence primer_1, primer_2)* | *pos_1 <- find position of primer_1 in sequence* | *pos_2 <- find position of primer_2 in sequence* | *amplicon length <- pos_2 + length(primer_2) - pos_1* | *return amplicon length* .. literalinclude:: _static/code/amplicon_len.py :linenos: :language: python :: >>> import sv40 >>> import fasta_to_one_line >>> >>> sequence = fasta_to_one_line(sv40) >>> print amplicon_len(sequence, first_primer, second_primer ) 199 :download:`amplicon_len.py <_static/code/amplicon_len.py>` . Exercise -------- reverse the following sequence "TACCTTCTGAGGCGGAAAGA" (don't compute the complement): :: >>> "TACCTTCTGAGGCGGAAAGA"[::-1] or >>> s = "TACCTTCTGAGGCGGAAAGA" >>> l = list(s) # take care reverse() reverse a list in place (the method do a side effect and return None ) # so if you don't have a obect reference on the list you cannot get the reversed list! >>> l.reverse() >>> print l >>> ''.join(l) or >>> rev_s = reversed(s) ''.join(rev_s) The most efficient way to reverse a string or a list is the way using the slice. Exercise -------- | The il2_human contains 4 cysteins (C) in positions 9, 78, 125, 145. | We want to generate the sequence of a mutatnt were the cysteins 78 and 125 are replaced by serins (S) | Write the pseudocode, before to propose an implementation: We have to take care of the string numbered vs sequence numbered: | C in seq -> in string | 9 -> 8 | 78 -> 77 | 125 -> 124 | 145 -> 144 | *generate 3 slices from the il2_human* | *head <- from the begining and cut between the first cytein and the second* | *body <- include the 2nd and 3rd cystein* | *tail <- cut after the 3rd cystein until the end* | *replace body cystein by serin* | *make new sequence with head body_mutate tail* il2_human = 'MYRMQLLSCIALSLALVTNSAPTSSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLTFKFYMPKKATELKHLQCLEEELKPLEEVLNLAQSKNFHLRPRDLISNINVIVLELKGSETTFMCEYADETATIVEFLNRWITFCQSIISTLT' :: head = il2_human[:77] body = il2_human[77:125] tail = il2_human[126:] body_mutate = body.replace('C', 'S') il2_mutate = head + body_mutate + tail Exercise -------- Write a function * which take a sequence as paramter * compute the GC% * and return it * display the results readable for human as a micro report like this: 'the sv40 is 5243 bp length and have 40.80% gc' use sv40 sequence to test your function. .. literalinclude:: _static/code/gc_percent.py :linenos: :language: python :: >>> import sv40 >>> import fasta_to_one_line >>> import gc_percent >>> >>> sequence = fasta_to_one_line(sv40) >>> gc_pc = gc_percent(sequence) >>> report = the sv40 is {0} bp length and have {1:.2%} gc".format(len(sequence), gc_pc) >>> print report 'the sv40 is 5243 bp length and have 40.80% gc' :download:`gc_percent.py <_static/code/gc_percent.py>` . :: gc_pc = float(sv40_sequence.count('g') + sv40_sequence.count('c')) / float(len(sv40_sequence)) "the sv40 is {0} bp lenght and have {1:.2%} gc".format(len(sv40), gc_pc)