第４章　変数と代入


ｖａｌｕｅが保存されている場所を保持している、
>>> a = 3 
>>> a
3

名前は a はvariable変数と呼ばれる。中身は変更できる。

ｖａｌｕａｂｌｅは value (3)を表示する。.

>>> s="葉桜の夕べ必ず風騒ぐ"
>>> ｓ
'葉桜の夕べ必ず風騒ぐ'


　変数に名前を付ける時は次のルール がある。
1) 1文字目は英文字かアンダーバー(_):日本語も可。


2) 2文字目以降は英数文字、アンダーバー：日本語も可。
3) 予約語は使用できない。
4) 大文字と小文字は区別される

５）名前の長さに制限はない。
６）変数名は利用の前に決めておかないとエラーになる。初期化しておく。
(http://www.pasteur.fr/formation/infobio/python/)　　
　　　ある値を変数に代入する。ａｓｓｉｇｎ
　　　変数にはオブジェクトが置かれてい
　　　る場所情報が格納されている。
　　　変数はオブジェクトのコピーでなく、リファ
　　　レンスを保持する。 
　　　Pythonでは変数の型はデータ入力時点で決まる。
　　　ほかのデータを代入すると元のデータは失われ、メモリ内から
　　　消去される。
　'

>>> a = 3 >>> a 3 This name is called a 'variable', because its value can change. Above, the interpreter displays the value (3) of the variable (a). >>> myVar = 'one sentence' >>> myVar 'one sentence' Variable names follow specific rules. See what happens below: >>> 1string = 'one string' File "<stdin>", line 1 1string = 'one string' ^ SyntaxError: invalid syntax >>> myvar Traceback (most recent call last): File "<stdin>", line 1, in ? NameError: name 'myvar' is not defined What happened? >>> a = 2 >>> a 2 >>> a * 5 10 >>> b = a * 5 >>> b 10 >>> a = 1 >>> b 10 Why hasn't b changed? >>> a = 1 in this case a is a number >>> a + 2 3 >>> a = '1' in this case a is a string >>> a + 1 Traceback (most recent call last): File "<stdin>", line 1, in ? TypeError: cannot concatenate 'str' and 'int' objects What do you conclude?

1.1.3. Strings

Some magical stuff, that will be explained later:

>>> from string import * 

We can also perform calculus on character strings:

>>> codon='atg'
>>> codon * 3
'atgatgatg'
>>> seq1 = 'agcgccttgaattcggcaccaggcaaatctcaaggagaagttccggggagaaggtgaaga'
>>> seq2 = 'cggggagtggggagttgagtcgcaagatgagcgagcggatgtccactatgagcgataata'


How do you concatenate seq1 and seq2 in a single string?


>>> seq = seq1 + seq2

What is the length of the string seq?

>>> len(seq)
120

Does the string seq contain the ambiguous 'n' base?
>>>  'n' in seq
False

Does it contain an adenine base?
>>> 'a' in seq
True

>>> seq[1]
'g'   

Why? 
Because in computer science, strings are numbered from 0 to string length - 1
so the first character is:
>>> seq[0]
'a'  

Display the 12th base.

>>> seq[11]
't'

Find the index of the last character.

>>> len(seq)
120

So, because we know the sequence length,  we can display the last character
by:
>>> seq[119]
'a'

But this is not true for all the sequences we will work on.
Find a more generic way to do it.

>>> seq[len(seq) - 1] 
'a'

Python provides a special form to get the characters from the end of a string:

>>> seq[-1]
'a'
>>> seq[-2]
't'

Find a way to get the first codon from the sequence
>>> seq[0] + seq[1] + seq[2]
'agc'

Python provides a form to get 'slices' from strings:
>>> seq[0:3]
'agc'

You can omit the first indice of the range if it's 0:
>>> seq[:3]
'agc'

>>> seq[3:6]
'gcc'



How would you access the slice of the 3 last characters?
Hints: you want the positions -3 -2 and -1. 
Do not forget that the last indice of the slice should be le last position + 1.

>>> seq[-3:len(seq)]
'ata'

You can omit the second indice of the range if it's len(seq):
>>> seq[-3:]
'ata'

How many of each base does this sequence contains?

>>> count(seq, 'a')
35
>>> count(seq, 'c')
21
>>> count(seq, 'g')
44
>>> count(seq, 't')
12

Count the percentage of each base on the sequence.
Example for the adenine representation

>>> long = len(seq)
>>> nb_a = count(seq, 'a')
>>> (nb_a / long) * 100
0

What happened? How 35 bases from 120 could be 0 percent?
This is due to the way the numbers are represented inside the computer.

>>> float(nb_a) / long * 100    
29.166666666666668

Now, let us say that you want to find specific pattern on a DNA sequence:

>>> dna = """tgaattctatgaatggactgtccccaaagaagtaggacccactaatgcagatcctgga
tccctagctaagatgtattattctgctgtgaattcgatcccactaaagat"""
>>> EcoRI = 'GAATTC'
>>> BamHI = 'GGATCC' 

Looking at the sequence you will see that EcoRI is present twice and
BamHI just once:

tgaattctatgaatggactgtccccaaagaagtaggacccactaatgcagatcctgga
 ~~~~~~                                                ~~~ 
tccctagctaagatgtattattctgctgtgaattcgatcccactaaaga
~~~                          ~~~~~~

>>> count(dna, EcoRI)
0

Why ??

>>> 'atgc' == 'atgc'
True
>>> 'atgc' == 'gcta'
False
>>> 'atgc' == 'ATGC'
False

why are 'atgc' and 'ATGC' different?

We can convert the case of a string:

>>> EcoRI = lower(EcoRI)
>>> EcoRI
'gaattc'
>>> count(dna, EcoRI)
2
>>> find(dna, EcoRI)
1
>>> find(dna, EcoRI, 2)
88
>>> BamHI = lower(BamHI)
>>> count(dna, BamHI)
0

Why ?

Tip: display the sequence:

>>> dna
'tgaattctatgaatggactgtccccaaagaagtaggacccactaatgcagatcctgga\ntccctagctaagatgtattattctgctgtgaattcgatcccactaaagat'

What is this '\n' character?

How to remove it?

>>> dna = replace(dna, '\n', '')
>>> dna
'tgaattctatgaatggactgtccccaaagaagtaggacccactaatgcagatcctggatccctagctaagatgtattattctgctgtgaattcgatcccactaaagat'
>>>find(dna, BamHI)
54  

Using the mechanisms we have learnt so far, produce the complement of
the dna sequence.

参照　パリ　インスチュール研究所ｗｅｂより

1.1.2. Variables

1.1.3. Strings

1

参照 パリ インスチュール研究所ｗｅｂより

1.1.2. Variables

1.1.3. Strings

1

参照　パリ　インスチュール研究所ｗｅｂより