one of the most important and unique feature of python, which made me start using it, is the fancy print() function. Grab any introductory book (like: Beginning programming in python for dummies ) about Python 3 and it tells you that you can write a software by printing ("hello world !") on the screen. So let's start using this function to print out certain fancy biological data on the screen.
what the above code does is that it puts "TCGATG" in the DNA variable. Then the print() function shows it on the screen. So, whenever you write print(DNA) it shows you the content of DNA variable which is TCGATG .
It is important to know a little about variables as well, and variables are virtual boxes that can hold different types of data.
there are several types of variables which are basically String "for text", Integer for whole numbers, boolean for True and False data, as well as float for data with decimal numbers or fractional values. The DNA variable holds a string which is a text datum.
Since python 3 uses print() as function you can do so many tasks with it, I am going to show few below:
1- reversing a string:
you may want to get the reverse of a DNA strand, and you can do that in python using a single line of code by typing
>>> print(DNA[::-1])
the result would be as follows:
GTAGCT
which is the reverse of TCGATG
this is quite handy and if you use other programming languages to do the same it would take you a while to figure out how to do so.
2- you can concatenate your data with a text to provide information about the data shown as an output.
>>> print ("this is your DNA sequence", DNA)
this is your DNA sequence TCGATG
3- you can write tandems of your DNA sequence by simply multiplying your text by the number of times you would want that tandem to appear.
>>> print(DNA *2)
TCGATGTCGATG
4- you can transform a variable into a list by inserting [ ] in the print function.
>>> print([DNA])
['TCGATG']
it is quite important to use lists while writing functions/ or methods for bioinformatics tools and software as it helps iteration easier and more reliable [read about iteration over strings in: Python recipes handbook by Joey Bernard].
5- if you would like to make every item of your DNA variable a list item use the following code block:
NOTE: this is a for loop , and it basically iterates over the items of the string, then makes each item a list item and finally separates them with a , the end = ',' command is what separates the list items from one another.
6- you might also want to start counting nucleotides in a DNA sequence. To do so, use the following line of code:
>>> print("your DNA sequence contains", DNA.count("A"),"Adenine")
your DNA sequence contains 1 Adenine
7- using if statements is another useful way to print out your results.
>>> if True:
print(DNA.count("T"))
2
8- one can also use .split() function inside print() function to split a string into lists of desirable length. This would work based on the number of spaces that are there within your string. In this case NONE.
>>> print(DNA.split())
['TCGATG']
split strings could also be joint by .join() function.
for instance:
>>> a = "+" # this is a variable that holds + as a datum
>>> seq = ("A","T","G","C") # this is another variable that holds A,T,C,and G as as data
>>> print(a.join(seq))
A+T+G+C
what the above code does is that it puts "TCGATG" in the DNA variable. Then the print() function shows it on the screen. So, whenever you write print(DNA) it shows you the content of DNA variable which is TCGATG .
It is important to know a little about variables as well, and variables are virtual boxes that can hold different types of data.
there are several types of variables which are basically String "for text", Integer for whole numbers, boolean for True and False data, as well as float for data with decimal numbers or fractional values. The DNA variable holds a string which is a text datum.
Since python 3 uses print() as function you can do so many tasks with it, I am going to show few below:
1- reversing a string:
you may want to get the reverse of a DNA strand, and you can do that in python using a single line of code by typing
>>> print(DNA[::-1])
the result would be as follows:
GTAGCT
which is the reverse of TCGATG
this is quite handy and if you use other programming languages to do the same it would take you a while to figure out how to do so.
2- you can concatenate your data with a text to provide information about the data shown as an output.
>>> print ("this is your DNA sequence", DNA)
this is your DNA sequence TCGATG
3- you can write tandems of your DNA sequence by simply multiplying your text by the number of times you would want that tandem to appear.
>>> print(DNA *2)
TCGATGTCGATG
4- you can transform a variable into a list by inserting [ ] in the print function.
>>> print([DNA])
['TCGATG']
it is quite important to use lists while writing functions/ or methods for bioinformatics tools and software as it helps iteration easier and more reliable [read about iteration over strings in: Python recipes handbook by Joey Bernard].
5- if you would like to make every item of your DNA variable a list item use the following code block:
NOTE: this is a for loop , and it basically iterates over the items of the string, then makes each item a list item and finally separates them with a , the end = ',' command is what separates the list items from one another.
6- you might also want to start counting nucleotides in a DNA sequence. To do so, use the following line of code:
>>> print("your DNA sequence contains", DNA.count("A"),"Adenine")
your DNA sequence contains 1 Adenine
7- using if statements is another useful way to print out your results.
>>> if True:
print(DNA.count("T"))
2
8- one can also use .split() function inside print() function to split a string into lists of desirable length. This would work based on the number of spaces that are there within your string. In this case NONE.
>>> print(DNA.split())
['TCGATG']
split strings could also be joint by .join() function.
for instance:
>>> a = "+" # this is a variable that holds + as a datum
>>> seq = ("A","T","G","C") # this is another variable that holds A,T,C,and G as as data
>>> print(a.join(seq))
A+T+G+C
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