Next, we'll talk about communicating with the outside or, in other words, reading our data from files instead of requiring someone to type it in. Most of the time when you're doing genomic data science or any kind of data analysis, you're not actually typing in data at the terminal or asking someone else to input the data while your program is running. Usually, our data sets are far too big to do that. So we read our data from files which might be very large files. So let's go through, today we'll talk about how to go through data that comes from a file. To do that we need to open the file, do something to the file and then close the file. It's pretty simple. So to open a file, to read or write to the file, we use the built-in function in Python called open. So let's look at an example. To read from a file, we would just call the file, say f, okay, very simple name. We say f=open('myfile'), and where myfile would be the name of the file in your file system. And we would give it the string r in single quotes, just the letter r, which says I'm going to open this file and read from it. So r is the default mode, default value for the open function, so we don't have to include that. We can just say f equals open my file. If we want to write to a file though that's not the default. So we would say we could say f equals open my file and provide the second argument function the letter w, which means we're going to write to this file. If we do that, then as soon as we start writing to the file we'll be creating a new version of this file, overriding anything that's already in it. Sometimes we don't want to do that because we have some big file. And suppose we want to just add to it. So we can open the file on a third way in append mode using the special character a as the argument to the open function. And a says we're going to append whatever we write to the file, get to the end of our existing file so we don't destroy what's already there. So if you attempt to open a file that does not exist Python's going to give you an error. So let's see what happens, we type f equals open my file. Myfile, let's say you typed it wrong or that file doesn't exist, Python's just going to give you an error. Now you don't really want that to happen in the middle of your program. But you can check before opening a file or when opening a file to see if it exists, looking at the special variable built into Python in the following way. We write try:, so that's a special command, try, f = open("myfile"). And if it doesn't work, then Python returns this special exception code called IOError. So we write except, that's also a special keyword, IOError where I, O, and E are all in capital letters. And after IOError we write colon and then print out an answer message. So what this special syntax does is it tries a function. Here it's trying out opening a file and if I get an error back from the operating system then Python is going to just print out a message. So instead of just crashing, it's going to print a message. And so it won't print an error message and instead now this time it will print out the file myfile does not exist. That's a little more useful than the error message that Python might give you. So now let's talk about reading from a file. So suppose that myfile contains two lines. The first line is called, it just says this is the first line of the file, and the second line says second line of the file. So this is a simple text file, it has two lines in it. So a simple and fast way to read the content of the file is to just loop over the object. So we've already opened the file, so now we can type for line in f, so this is a sort of special syntax of for. We're now iterating through this file object that we returned one line at a time and we can just print it out. So this syntax here this for loop here will simply go through the file and print out each line so you see here's the output which is just each line of the file printed out one at a time. You can also read the content of a file using the read method of the file object. So I can type f.read() which invokes the read method with no arguments. And it invokes that method on the file, f. Now, notice if I just typed it here in this sequence that it doesn't return anything. That's because we just finished reading that file, so that file object now points to the end of the file. There's nothing left to print, so when I try to read it, there's nothing left to read. So we can adjust that though. By using the special f.seek() function. So we can change our position within a file object. So after reading all the lines in a file we're at the end of it. Suppose we want to go back to the beginning and read it again. We can use the method seek on the file object f and tell it where to go. So to do that we could say f.seek(0) and that says go to a position zero, to the beginning of file. And that returns as you see returns the value zero signifying that we're at the beginning of the file. And now if I wanted to read the file again, using f.read(), I would actually get the entire file. So f.read() unlike the previous syntax doesn't go to the file a lot of the time but it actually reads the whole file. So what it returns here is the entire file, which you see is two lines including the new line characters. So you sometimes don't want to do that, you usually want to read just one line at a time. So I can use a special built-in method readline to read one line at a time as well. So I could say f.seek(0), that says go back to the beginning of the file. So now f.readline() will just read one line from the file and that returns the value of the first line of the file. Similarly I can write a line of the file, so here's our file with three lines in it. So if I used the write method that'll write the contents of a string to a file, returning the number of characters that it just wrote for Python 3.x or returns just none in Python 2.x. So let's open our file myfile in append mode so here's the command for that. F equals open. And then we get the full path to the filename and the character a, which says we're going to append to it. And now we do f.write() and give it the string. This is a third line. And in Python 3.x, which we're using here, that'll return 20, which is the number of characters we just wrote. And what happens is it just wrote that third line to our file. So now our file is one line longer than it was than it was before. Finally when you are done with a file you want to close it. So for that you use the close method with no arguments. We just call it f.close(). It closes the file and frees up any system resources taken up by the open file. In general if you forget to close a file at the end of your program, it'll be closed when the program exits. But it's a good programming practice to close it explicitly by calling f.close(). So if we called f.close(), and then we try to read the file again, the file f again, we would get an error, and that's because the file's no longer open. In the next lecture, we're going to talk about, we're going to show how to use these commands to actually read this file containing some DNA sequences and do something useful with it.
