If statements in Python are similar in form to Bash, but simpler. The general form is
if <CONDITION>:
<DO_THIS>
The if statement has to finish with a :. Also, in Python, the code block inside the if statement must be indented. You can use either tabs or a certain number of spaces. When using spaces, you must use the same number of spaces throughout your code. The official recommendations for Python style strongly suggest using 4 spaces, rather than tabs.
The syntax for logical tests is quite intuitive in Python. To test equality, use two equals signs, ==.
myStr == "some text"
You can test if two things are not equal with !=.
myStr != "other text"
if statements can be used on their own, but no code will be executed when the condition is false.
To include code blocks that should be executed when the condition is false, you'll need to use an if...else statement. These have the general form:
if <CONDITION>:
<DO_THING_WHEN_TRUE>
else:
<DO_THING_WHEN_FALSE>
Sometimes, you'll want to test a series of conditions to decide what to do. In that case you could use a nested set of if...else statements:
nuc = "A"
if nuc == "A":
print("Nucleotide is an A.")
else:
if nuc == "C":
print("Nucleotide is a C.")
else:
if nuc == "G":
print("Nucleotide is a G.")
else:
if nuc == "T":
print("Nucleotide is a T.")
However, you'll notice that this can get pretty cumbersome pretty quickly. Thankfully, python offers another, more compact, way to write this:
nuc = "A"
if nuc == "A":
print("Nucleotide is an A.")
elif nuc == "C":
print("Nucleotide is a C.")
elif nuc == "G":
print("Nucleotide is a G.")
elif nuc == "T"
print("Nucleotide is a T.")
The elif statements stand for else...if and capture what we tried to do above with the nesting.
It is important to realize that as we've currently written these statements, nothing would happen if the variable nuc didn't have the value A, C, G, or T. This can be a big problem when accepting input from a user or file that might provide an unintended value. To capture these cases, it's always best to close with a simple else:
nuc = "A"
if nuc == "A":
print("Nucleotide is an A.")
elif nuc == "C":
print("Nucleotide is a C.")
elif nuc == "G":
print("Nucleotide is a G.")
elif nuc == "T":
print("Nucleotide is a T.")
else:
print("This is not a valid nucleotide!")
We've now covered the simple variable types in Python: integers, floats, strings, and bools. However, there are several more complex types of variables that allow us to store and access multiple values. Perhaps the most versatile and common of these more complex types are lists. Lists are always specified using square brackets - [].
Lists can contain an arbitrary number and type of simpler variables, but we often want to use only one type in a list so as not to get confused.
listOfNums = [1,2,3,4]
listOfFloats = [3.14, 2.0, 12.3]
listOfStrings = ["Ecology", "Evolution", "Systematics"]
listOfBools = [True, False, False, True]
Even after they are created, lists can be modified. Individual elements can be added using the .append() method:
listOfNums.append(5)
listOfStrings.append("Neurobiology")
Take another look at these lists
listOfNums
listOfStrings
Elements can be removed using a few different methods. Try
listOfFloats.pop()
What is returned? And what does the list look like now?
You can remove specific values from a list, regardless of their position, by using the remove(<VALUE>) method. What happens when you execute
listOfBools.remove(False)
How does the list change?
Lists can contain lists as elements. For instance, try this:
newList = []
newList.append([1,2,3])
newList.append([4,5,6])
newList.append([12,13,14])
What does newList look like now?
newList
You can also add all the individual elements of one list to another.
newList = [1,2,3]
newList.extend([4,5,6])
newList.extend([12,13,14])
How does this version of newList differ from what you got when you used append()?
You can view or extract parts of a list by using indices and "slicing" the list (just remember that Python starts counting at 0!)
newList[4:7]
What values are returned? How do these relate to the indices you provided?
You can also alter individual elements of lists by using indices
newList
newList[2] = 100
newList
One of the nicest things about Python is the relationship between lists and for loops. If you have an existing list, you can quickly iterate across all of its elements using this syntax:
for num in newList:
print("This number is: %d" % num)
If you still want to iterate over a series of integers, you can use the range() function.
for num in range(10):
print("This number is: %d" % num)
Try this
firstNum = 2
secondNum = firstNum
firstNum = 5
firstNum
secondNum
How do firstNum and secondNum compare to each other? Now try this
firstList = [1,2,3]
secondList = firstList
firstList.extend([4,5,6])
firstList
secondList
How do firstList and secondList compare?
To read or write from a file, you'll first need to define the file name
inFileName = "FileToRead.txt"
However, this is just a string variable with the file name. We need to create an object that can actually read the contents of a file. Python has a built-in function to create a file object
open(<FILENAME>,<MODE>)
The <FILENAME> argument is just a string with the file's name (or path to the file). The <MODE> argument tells Python whether we are reading from a file (r), writing to a file (w), or appending to a file (a). To open up a new File object to read file contents, use syntax like this
inFile = open(inFileName,'r')
There are several useful methods associated with file objects, but one of the most commonly used is readline(). This method will read lines one-by-one from the file. Note that the end of line character (\n) is retained when the line is read in.
firstLine = inFile.readline()
Files opened for reading can be used in a for loop, as follows, to go through all the lines in the file
for line in file:
print("Length of line is: %d" % (len(line)))
Note that line is just a variable name we've chosen to hold each line as we iterate through the file. You can use any variable name you choose, as with any other for loop.
Writing to a file is very similar to reading from a file. First, you define an output file name
outFileName = "FileToWrite.txt"
To create a file object to use for writing, we'll again use the open() function, but we'll specify 'w' for the <MODE>.
outFile = open(outFileName,'w')
To write to the file line-by-line, we can use the .write() method.
outFile.write("This is a new sentence.\n")
Note that the write() method does NOT, by default, add a new line character to strings. If we want to end a line, we have to explicitly include \n.
As with bash scripts, Python scripts can also take advantage of command-line arguments. To easily handle command-line arguments, we're going to take advantage of some functions in the sys library. So we'll need to start by importing that library:
import sys
Any command-line arguments we pass to a script can then be accessed using the sys.argv variable. For instance
print(sys.argv[2])
Practice Exercise
(1) Create a Python script that loads the
syslibrary(2) Include the print statement above
(3) Execute the script with several command-line arguments (
myScript.py one 2 THREE 4 five SIX)Which argument is printed when you run the line above?
We can also loop through all command-line arguments:
for arg in sys.argv:
print(arg)
These abilities are very useful in a variety of contexts, but particularly when a set of filenames are provided as command-line arguments and you want to iteratively process each file.