Welcome+to+Unix

=Genomic Analysis at the UNIX Command Line=

Your instructors are: Aaron Hardin and Chris Ellison.

IMPORTANT NOTE
The material below is intended for the in-class instruction. Others trying to learn this material offline can follow along on any Unix machine, however, please be aware the file names and path names will be different on your machine.

Topics covered in this module:

 * Why familiarity with UNIX is necessary for genomic analyses
 * Navigating the UNIX environment
 * Basic UNIX utilities
 * Text editors
 * Basic data manipulation with UNIX

Introduction and Requirements
Welcome to the CGRL module for Genomic Analysis at the UNIX command line. This module is designed for scientists hoping to analyze genomic datasets, but who have no experience with the UNIX computing environment or common genomic analysis tools.

The module requires that you use a recent MacOS or Linux based system. Future versions of the module may accomodate Microsoft Windows users.

It is also expected that you have signed up for an account on the CGRL computing resources. If this is not the case, please raise your hand now.

What are you going to learn?
After this morning's session, you will be able to navigate the UNIX environment, allowing you to create, manipulate, and store large data files efficiently. You will find that in many ways, the UNIX environment is designed for speed and simplicity in using large files in a way that is unavailable in more "user-friendly" environments like Microsoft Windows or Mac OS. We will conclude this morning's session with a set of exercises that demonstrate the power of the UNIX environment to generate a basic description of the //Saccharomyces cerevisiae// genome.

In this afternoon's session, we will extend this morning's lessons to cover a common utility used in high-throughput sequencing, the Bowtie short-read aligner. After this afternoon, you should be able to generate proper output with the Bowtie aligner, and generate a description similar to the one we'll see in this morning's exercise.

What are you not going to learn?
This module is intended to teach very basic skills for the UNIX environment, allowing students to pursue more instruction with other modules that will guide you through the complications and considerations for proper genomic analysis. Accordingly, we will demonstrate the very basics of using one genomic utility (Bowtie), but we will not venture into the algorithms, the considerations, or the statistics behind a proper analysis. We hope that you are interested enough after finishing this module to pursue those questions with our other instructors.

Schedule for today
We are dividing today's module into two segments, each with time dedicated to practical exercises, and with an hour lunch break in between. Given the limited time allotted to cover today's material, it is important that we stay on schedule are return promptly from our break.

Warning: Learning curve ahead!
If you're unfamiliar with a text-based computing environment (some of us are old enough to have started with one as a kid), things may seem a bit archaic at first. That's okay, because UNIX is more than a bit archaic. It's not your fault. So if things seem opaque or difficult to remember, don't fret, and please feel free to ask us questions. In addition, you may want to queue up a couple of websites for quick reference. For example, [|this Unix Quick Reference] might be of use if you want to search for key words to remind you which command does what.

In the longer term, you may appreciate the following text available to us via the UC Berkeley Library: Linux Pocket Guide

Using the UNIX shell
Your time in the UNIX environment will be spent in the **shell**, which is lingo for the Terminal window, if you're using Mac OS. The shell allows you to move and copy files, run programs, and more. We will also touch on the basic usage of two popular text editors, **emacs** and **vi**.

Informative Interlude: Some notes on the formatting of the lessons for this course
Periodically, we may stop with an **informative interlude** outlined with a horizontal line above and below (like the one two lines up!). In this case, we're taking a quick break to discuss this and other aspects of the formatting.

For this and all further examples, a **$** represents your shell prompt, and **boldface** indicates the commands to type at the prompt. //Italics// will be used for output you should see when you take the described action.

This concludes our first informative interlude.

How do I open my terminal window?
In Mac OS, you can open a new terminal window by opening the Finder, selecting the Applications folder, then the Utilities sub-folder, and then double-clicking on the Terminal application. You may want to drag the Terminal icon to your Application Dock for ready access going forward.

Alternatively, you can just use Spotlight to search for "Terminal" each time, and open the application after it is listed in the Spotlight results list.

In Linux environments, your terminal program will depend on the version of Linux you have installed. If you are using Linux and you don't know how to open a terminal, raise your hand and let us know now.

Accessing your CGRL account
The next step is to login to the CGRL system (poset.cgrl.berkeley.edu) with your user account and password. You can do this with the **ssh ** command.

$ **ssh aihardin@poset.cgrl.berkeley.edu**

Whoa, where am I?
When you first log into a system, you should be placed in your **home directory**. This is a special directory on the system meant just for you.

You can use the **pwd ** command to see the location of the directory you're in, whether it's your home directory or any other directory you end up navigating.

$ **pwd**

///global/home/aihardin//

And you can use the **cd ** command to change to another directory.

$ **cd /global**

$ **pwd** ///global//

To return to our home directory, we can simply change back.

$ **cd /global/home/aihardin**

$ **pwd** ///global/home/aihardin//

Although there is a shortcut for returning to your home directory from any other directory, which is to simply issue the **cd** command with no directory argument:

$ **cd**

$ **pwd** ///global/home/aihardin//

Another useful shorthand for **cd** is to use two dots after the command. This will take you one directory "up" in the tree. For example, if we want to go to **/global/home** from our home directory, we can just issue:

$ **cd ..**

$ **pwd** ///global/home//

And we can go all the way the to the top, or **root**, of the file system tree if we issue this command again.

$ **cd ..** $ **cd ..**

$ **pwd** /

But being that far from home might make us nervous, so with one quick command we can go back to our home directory.

$ **cd**

$ **pwd** ///global/home/aihardin//

Whew. That's better.

An aside on directories...

Directories in UNIX are set up the same way as any other computer. Just as you would open up a window into your directories and click to open up folders, here you use **cd** to go through the directories. You are just typing the command instead of clicking!

And if we want to find out what files are available in each folder, we have the command **ls**.

$ **ls **

Of course, we have to have files if we want to see them.

$ **ls /global/home** //aalmeida aminoda cbendix dhuang fzapata hrichard jtaylor khayden ktakahas mguising nkong sbranco tlee ylin// //adarob apfeiffe cellison dkhendrix ganeshm jaspden jtepperm khockett lpu mstrzele pimentel scolmena tlevin yzhang// //aihardin bdebebe cschartn epurdom gergana jcraig jyoung kkim mcohn msuarez rbart sruddy tyamaguc zsung// //akassen bwheeler dchandra ewhiston hgoodman jstillma kbenton kmuriki mdavis mtaliafe rthomas tkaplan xfeng//


 * ls** has many options. Here are some of the more useful ones to know.

The **-l** argument shows the detailed list of the files. This is similar to the options you're likely familiar with in MacOS or Windows.

$ **ls -l**

The **-t** argument will sort the files by their modification time, so you can see which file is the newest (first) or oldest (last) in the directory list.

$ **ls -lt**

What does the **-r** argument do?

$ **ls -ltr**

The same directory short hand for the directory above us in **cd** can be used for **ls**:

$ **ls ..** //aalmeida aminoda cbendix dhuang fzapata hrichard jtaylor khayden ktakahas mguising nkong sbranco tlee ylin// //adarob apfeiffe cellison dkhendrix ganeshm jaspden jtepperm khockett lpu mstrzele pimentel scolmena tlevin yzhang// //aihardin bdebebe cschartn epurdom gergana jcraig jyoung kkim mcohn msuarez rbart sruddy tyamaguc zsung// //akassen bwheeler dchandra ewhiston hgoodman jstillma kbenton kmuriki mdavis mtaliafe rthomas tkaplan xfeng//

"To create is divine..."
We can make new directories with the command **mkdir**.

$ **mkdir myFirstDirectory**

And then, of course, we can change to that directory.

$ **cd myFirstDirectory**

And we can use the **touch** command to make our first file.

$ **touch myFirstFile**

$ **ls** //myFirstFile//

The command **echo** repeats whatever we tell it to (make sure to use single quotation marks).

$ **echo 'Hello, World!'** //Hello, World!//

And we can use it to add contents to our new file if we **redirect** the output with the **>** arrow.

$ **echo 'Hello, World!' > myFirstFile**

Then to view the contents, we can use the **cat ** command.

//Hello, World!//
 * $ cat myFirstFile**

"...to reproduce is human."
Often, we will merely want to copy or move existing files.

To copy, we use the command **cp**.

$ **cp myFirstFile mySecondFile**

$ **ls -lt** //-rw-r--r-- 1 matt matt 14 Sep 5 14:22 mySecondFile// //-rw-r--r-- 1 matt matt 14 Sep 5 14:16 myFirstFile//

Or, maybe we just want to move (i.e. rename) the file with the **mv** command.

$ **mv myFirstFile myRenamedFile**

But no worries if you change your mind, you can always move it back.

$ **mv myRenamedFile myFirstFile**

Peeking inside files
For the following examples, we're going to need a bit more text in our file. Since we're genomicists, we may as well use a FASTA file.

code > seq1 This is the description of my first sequence. AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT CGACGTAGATGCTAGCTGACTCGATGC > seq2 This is a description of my second sequence. CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC CATCGTCAGTTACTGCATGCTCG > seq3 and so on... GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG > seq4 CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC GTAGATGCTAGCTGACTCGAT

code

Let's start by copying this text by highlighting.

Then we'll echo the entire block to a new file. We have to add the first and last quotation marks, the **>** arrow, and the name of our new file we're echoing the text to, **test.FASTA**

$ **echo '> seq1 This is the description of my first sequence.**
 * AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA**
 * TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT**
 * CGACGTAGATGCTAGCTGACTCGATGC**
 * >seq2 This is a description of my second sequence.**
 * CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG**
 * GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC**
 * CATCGTCAGTTACTGCATGCTCG**
 * >seq3 and so on...**
 * GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT**
 * CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT**
 * AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG**
 * >seq4**
 * CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG**
 * GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC**
 * GTAGATGCTAGCTGACTCGAT' > test.FASTA**

Now we can check to make sure the file looks we want it to with the cat command.

//> seq1 This is the description of my first sequence.// //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT// //CGACGTAGATGCTAGCTGACTCGATGC// //> seq2 This is a description of my second sequence.// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //CATCGTCAGTTACTGCATGCTCG// //> seq3 and so on...// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT// //CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT// //AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG// //> seq4// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTAGATGCTAGCTGACTCGAT//
 * $ cat test.FASTA**

We've seen how to use the **cat** command to dump the contents of a file to the screen, but there is a slightly more sophisticated utility, **less**.

//> seq1 This is the description of my first sequence.// //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT// //CGACGTAGATGCTAGCTGACTCGATGC// //> seq2 This is a description of my second sequence.// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //CATCGTCAGTTACTGCATGCTCG// //> seq3 and so on...// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT// //CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT// //AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG// //> seq4// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTAGATGCTAGCTGACTCGAT// //test.FASTA (END)//
 * $ less test.FASTA**

Here are some useful navigational tips for **less**:
 * You can use the arrow keys to move up or down a line in the text.
 * The spacebar will advance an entire page.
 * You can search for a word by typing a slash (e.g. **/)** followed by the search word.
 * To quit, type **q**.
 * To see the full help screen, type **h**.

Informative Interlude: UNIX names tend to be overly clever
As you've seen with the basic commands thus far, the names are generally descriptive abbreviations of the program's function. For example, **mkdir** is for making a directory, **ls** is for listing the contents of a directory, etc. However, programmers, especially UNIX programmers, tend to get increasingly clever as things progress. Unaware of the fact that this practice makes things opaque, the typically programmer cries out for attention by making program names self-referentially clever. **less** is a good example of this. In the olden days, the most basic ways to view a text file could not divide files into individual pages, thus a multipage document would scroll off the screen before the first page could be read. As a solution, a program called **more** was written, which paused at the bottom of each page and prompted the user to press the spacebar for "more." The program name here is reasonably descriptive, but **more** had some noticeable feature deficiencies: you could neither advance the text one line at a time nor navigate backward in the document without reloading the whole file. The program written to accommodate these features is **less**. The cleverness of the name is revealed by the paradoxical adage "[|less is more] ."

By default, the **head** command prints the top 10 lines of the input file. To print a different number, say 5, lines:

$ **head test.FASTA** //> seq1 This is the description of my first sequence.// //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT// //CGACGTAGATGCTAGCTGACTCGATGC// //> seq2 This is a description of my second sequence.// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //CATCGTCAGTTACTGCATGCTCG// //> seq3 and so on...// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT//

$ **head -5 test.FASTA** //> seq1 This is the description of my first sequence.// //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT// //CGACGTAGATGCTAGCTGACTCGATGC// //> seq2 This is a description of my second sequence.//

And if you should want to see the end of the file, you can use the **tail** command.

$ **tail** **test.FASTA** //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //CATCGTCAGTTACTGCATGCTCG// //> seq3 and so on...// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT// //CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT// //AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG// //> seq4// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTAGATGCTAGCTGACTCGAT//

As I alluded to earlier, the **cat** command stands for **concatenate**, and though we were using it to view the contents of a single file, it was originally intended to do just what its name suggests: put multiple files together.

$ **cat** **mySecondFile test.FASTA** //Hello, World!// //> seq1 This is the description of my first sequence.// //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT// //CGACGTAGATGCTAGCTGACTCGATGC// //> seq2 This is a description of my second sequence.// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //CATCGTCAGTTACTGCATGCTCG// //> seq3 and so on...// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT// //CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT// //AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG// //> seq4// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTAGATGCTAGCTGACTCGAT//

More Utile Utilities
At this point, you may be thinking to yourself, "Hrmmm.... This is all well and good, Mr. Computerpants, but it sure seems like a lot of trouble to go through just to read and write some sequences to a text file. I could have done this at home!" And if so, I say it's hard to blame you. But that's because we're just getting to the good part.

Maybe you were wondering, "Gosh, I wish I could search one of these sequence files for a particular sequence without having to open up a Word document or spreadsheet!" Never fear, **grep ** is here.


 * grep** searches for the a string of text in a file and prints out all lines where it finds the specified text.

$ **grep seq test.FASTA** //> seq1 This is the description of my first sequence.// //> seq2 This is a description of my second sequence.// //> seq3 and so on...// //> seq4//

If you wanted to see how many lines contain your query, you can give **grep** the **-c** argument.

$ **grep -c seq test.FASTA** //4//

The **-v** argument inverts the search (i.e. prints lines that //do not// contain your search string).

$ **grep -v seq test.FASTA** //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT// //CGACGTAGATGCTAGCTGACTCGATGC// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //CATCGTCAGTTACTGCATGCTCG// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT// //CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT// //AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTAGATGCTAGCTGACTCGAT//

Some of the basic functions you would use a complicated speadsheet for can be acheive with the utility **sort**, which true to its name, sorts the line in a file.

//> seq1 This is the description of my first sequence.// //> seq2 This is a description of my second sequence.// //> seq3 and so on...// //> seq4// //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG// //CATCGTCAGTTACTGCATGCTCG// //CGACGTAGATGCTAGCTGACTCGATGC// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTAGATGCTAGCTGACTCGAT// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT//
 * $ sort test.FASTA**

The next utilities we will cover only with a description, but keep them in mind, because it will help you in the exercises later this morning.

Imagine that you have a spreadsheet worth of data, and that you only want to consider the third column of the spreadsheet. Instead of opening Excel and copying and pasting your column to a new file, you could use the **cut** utility.

$ **cut -f 3 filename**

This command will return only the third column from a tab-delimited file.

Wildcard Matching with the asterisk ( * )
You may want to use a utility on multiple files, which is possible using the * wildcard character. The simplest example of this is using **ls** to list multiple files.

$ **ls** //myFirstFile mySecondFile test.FASTA//

$ **ls *File** //myFirstFile mySecondFile//

$ **ls myF*File** //myFirstFile//

In these examples, we can see that the asterisk will match any set of intervening characters.

Controlling Information Flow with the Pipe
UNIX has several features that have no good analogous function in other operating systems, and one such commonly used feature is called the Unix **pipe**. Often, you will want to use several utilities serially in one process. The **pipe ** allows you to send the output of one program as the input to the next program automatically.

The **pipe** character is the **|** located above the backslash key.

If we wanted to search the a list of files, we could send the output of **ls** to **grep** with a **pipe**.

$ **ls -lt | grep my** //-rw-r--r-- 1 matt matt 14 Sep 5 14:22 mySecondFile// //-rw-r--r-- 1 matt matt 14 Sep 5 14:16 myFirstFile//

Here, we see the two files in our directory listing that contain the search term "my" returned by **grep.**

**Redirection**
Another built-in UNIX tool is called **redirection**, and we've already seen it once today (I just didn't bother to explain it earlier!).

When we copied and pasted our sequences to **test.FASTA**, we used **redirection** with the **>** arrow.

$ **cat myFirstFile test.FASTA mySecondFile > myCombinedFile**

$ **cat myCombinedFile** //Hello, World!// //> seq1 This is the description of my first sequence.// //AGTACGTAGTAGCTGCTGCTACGTGCGCTAGCTAGTACGTCAA// //TCGTACGTCGACTGATCGTAGCTACGTCGTACGTAGGTACGTT// //CGACGTAGATGCTAGCTGACTCGATGC// //> seq2 This is a description of my second sequence.// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //CATCGTCAGTTACTGCATGCTCG// //> seq3 and so on...// //GATCGTACGTGTAGCTGCTGTAGCTGATCGTACGGTAGCAGCT// //CGTCGACTGATCGTAGCTGATCGTACGTCGACTGATCGTAGCT// //AGTACGTAGTAGCTGTAGCTGATCGTACGTAGCTGATCGTACG// //> seq4// //CGATCGATCGTACGTCGACTGATCGTAGCTACGTCGTACGTAG// //GTACGTGATCGTACGTCGACTGATCGTAGCTATCGTAGCTACC// //GTAGATGCTAGCTGACTCGAT// //Hello, World!//

We can see from this example that the **redirection** arrow tells UNIX to send the output of the command to a file, instead of the screen.

Downloading Files
Instead of using your web browser to download files from a data resource like NCBI, in UNIX, we have efficient command line utilities for retrieving files. There are many tools for this purpose, but we'll use one common one, **wget** to retrieve files containing the sequences of the yeast genome.

First, let's make a new directory, called **fasta_files.**

$ **mkdir fasta_files**

And then we'll change to the new directory.

$ **cd fasta_files**

Now we can use the **wget** command to retrieve the files from the UC Santa Cruz sequence archive.

$ **wget 'ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/chromosomes/*'** //--12:43:53-- ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/chromosomes/*// //=> `.listing'// //Resolving hgdownload.cse.ucsc.edu... 128.114.119.148// //Connecting to hgdownload.cse.ucsc.edu|128.114.119.148|:21... connected.// //Logging in as anonymous ... Logged in!// //==> SYST ... done. ==> PWD ... done.// //==> TYPE I ... done. ==> CWD /goldenPath/sacCer2/chromosomes ... done.// //==> PASV ... done. ==> LIST ... done.// //[ <=> ] 1,482 --.--K/s// //12:43:53 (214.76 KB/s) - `.listing' saved [1482]// //Removed `.listing'.// //--12:43:53-- ftp://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/chromosomes/2micron.fa.gz// //=> `2micron.fa.gz'// ...

Now, when we look at what's happened to our directory, we'll see a list of files:

$ **ls** //2micron.fa.gz chrII.fa.gz chrIX.fa.gz chrVI.fa.gz chrX.fa.gz chrXIII.fa.gz chrXVI.fa.gz// //README.txt chrIII.fa.gz chrM.fa.gz chrVII.fa.gz chrXI.fa.gz chrXIV.fa.gz md5sum.txt// //chrI.fa.gz chrIV.fa.gz chrV.fa.gz chrVIII.fa.gz chrXII.fa.gz chrXV.fa.gz//

All but two of these files contain the sequence from a chromosome. The README.txt file contains information about the files, and the **md5sum.txt** contains information that can be used to verify the integrity of the files (but we won't be concerned with this).

You'll notice that all of the other files end with a double file extension, **.fa.gz**. File extensions tell you what to expect to be in the file, and in this case they're telling you that the file contains fasta sequence (the .fa part), and that the file has been compressed with the **gzip** utility, which saves disk space. **gzip** is only of several utilities available for compression. Others you may encounter include **tar** and **bzip**, though there are more.

In order to use the files, however, we need to uncompress them with the utility **gunzip**. We'll do this once here, and the again in this morning's exercises.

$ **gunzip 2micron.fa.gz**

$ **ls** //2micron.fa chrII.fa.gz chrIX.fa.gz chrVI.fa.gz chrX.fa.gz chrXIII.fa.gz chrXVI.fa.gz// //README.txt chrIII.fa.gz chrM.fa.gz chrVII.fa.gz chrXI.fa.gz chrXIV.fa.gz md5sum.txt// //chrI.fa.gz chrIV.fa.gz chrV.fa.gz chrVIII.fa.gz chrXII.fa.gz chrXV.fa.gz//

Notice that the only change is the name of the file we uncompressed, **2micron.fa.gz** has become **2micron.fa**

And if we take a peak at the beginning of the file with **head**, we can see that indeed looks like a fasta file:

$ **head 2micron.fa** //ACCTGCGGGCCGTCTAAAAATTAAGGAAAAGCAGCAAAGGTGCATTTTTA// //AAATATGAAATGAAGATACCGCAGTACCAATTATTTTCGCAGTACAAATA// //ATGCGCGGCCGGTGCATTTTTCGAAAGAACGCGAGACAAACAGGACAATT// //AAAGTTAGTTTTTCGAGTTAGCGTGTTTGAATACTGCAAGATACAAGATA// //AATAGAGTAGTTGAAACTAGATATCAATTGCACACAAGATCGGCGCTAAG// //CATGCCACAATTTGGTATATTATGTAAAACACCACCTAAGGTGCTTGTTC// //GTCAGTTTGTGGAAAGGTTTGAAAGACCTTCAGGTGAGAAAATAGCATTA// //TGTGCTGCTGAACTAACCTATTTATGTTGGATGATTACACATAACGGAAC// //AGCAATCAAGAGAGCCACATTCATGAGCTATAATACTATCATAAGCAATT//

The UNIX Path and Environment Variables
There are a lot of things going on behind the scenes of your UNIX shell. For the most part, Mac OS and modern Linux distributions will shield you from these mechanics, but we want to make you aware of two important concepts: the **UNIX Path** and your **environment variables**.

If we issue the **env** command, we will get something similar to the following output.

$ **env** HOSTNAME=poset.cgrl.berkeley.edu TERM=xterm-color SHELL=/bin/bash HISTSIZE=1000 SSH_CLIENT=169.229.195.27 55475 22 SSH_TTY=/dev/pts/0 USER=aihardin LS_COLORS=no=00:fi=00:di=01;34:ln=01;36:pi=40;33:so=01;35:bd=40;33;01:cd=40;33;01:or=01;05;37;41:mi=01;05;37;41:ex=01;32:*.cmd=01;32:*.exe=01;32:*.com=01;32:*.btm=01;32:*.bat=01;32:*.sh=01;32:*.csh=01;32:*.tar=01;31:*.tgz=01;31:*.arj=01;31:*.taz=01;31:*.lzh=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.gz=01;31:*.bz2=01;31:*.bz=01;31:*.tz=01;31:*.rpm=01;31:*.cpio=01;31:*.jpg=01;35:*.gif=01;35:*.bmp=01;35:*.xbm=01;35:*.xpm=01;35:*.png=01;35:*.tif=01;35: MAIL=/var/spool/mail/aihardin PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin:/global/home/aihardin/bin INPUTRC=/etc/inputrc PWD=/global/home/aihardin/myFirstDirectory/fasta_files LANG=C MODULEPATH=/usr/Modules/modulefiles:/usr/cports/modulefiles/redhat-5.x86_64:/etc/modulefiles:/global/software/centos-5.x86_64/modules/modfiles LOADEDMODULES= SHLVL=1 HOME=/global/home/aihardin LOGNAME=aihardin SSH_CONNECTION=169.229.195.27 55475 169.229.192.160 22 MODULESHOME=/usr/Modules LESSOPEN=|/usr/bin/lesspipe.sh %s G_BROKEN_FILENAMES=1 module= { eval `/usr/Modules/bin/modulecmd bash $*` } _=/bin/env OLDPWD=/global/home/aihardin/myFirstDirectory

What we see here are the values assigned to many **environment variables**. These are variables defined in your **shell** to make it easier for UNIX to do what you ask. For example, you can see that the variable **USER** is defined as **aihardin**. UNIX knows what my name is :-) And that is actually required for me to do anything useful as a user. Similarly, you can see **HOME** is defined as **/global/home/aihardin**. This is what tells UNIX where my home directory is located. If we change this variable to another directory, and then I issue the **cd** command to take me home, it will take me to the newly specified directory instead of my original home directory.

Sometimes this list can be very long and difficult to read, but if we know what we're looking for, we can use other utilities to help us.

$ **env | grep home** //HOME=/global/home/aihardin// //MODULESHOME=/usr/Modules//

This afternoon we will modify an important **environment variable** called **PATH**. The **PATH** variable tells UNIX a list of directories that it should put on your favorites list. That is, a list of directories that you don't have to specify the whole name of in order to use the files within them. For example, when we issue the command **ls**, a the program that runs is actually located in a directory called **/bin/**, so the program that we're actually running is **/bin/ls**. However, since **/bin/** is in our **PATH** by default, UNIX knows that when we type **ls**, we really meant **/bin/ls**.

In fact, if we use the **env** command, we can see the list of directories that are in our **PATH**, and they are separated by colons.

$ **env | grep PATH** //PATH=/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/opt/dell/srvadmin/bin:/global/home/aihardin/bin// //MODULEPATH=/usr/Modules/modulefiles:/usr/cports/modulefiles/redhat-5.x86_64:/etc/modulefiles:/global/software/centos-5.x86_64/modules/modfiles//

Here we see 6 directories in my **PATH**, separated by colons in the list.

Help, I'm stuck!
Most commands have many useful flags beyond what we've shown you. For information on a particular command, look at the manual pages with **man**. code bash-3.2$ man ls

LS(1) BSD General Commands Manual LS(1)

NAME

ls -- list directory contents SYNOPSIS

ls [-ABCFGHLOPRSTUW@abcdefghiklmnopqrstuwx1] [file ...] DESCRIPTION For each operand that names a file of a type other than directory, ls displays its name as well as any requested, associated information. For each operand that names a file of type directory, ls displays the names of files contained within that directory, as well as any requested, asso- ciated information. If no operands are given, the contents of the current directory are dis- played. If more than one operand is given, non-directory operands are displayed first; directory and non-directory operands are sorted sepa- rately and in lexicographical order. The following options are available: -@ Display extended attribute keys and sizes in long (-l) output. -1 (The numeric digit ``one''.) Force output to be one entry per line. This is the default when output is not to a terminal. -A List all entries except for. and ... Always set for the super- user. -a Include directory entries whose names begin with a dot (.). -B Force printing of non-printable characters (as defined by ctype(3) and current locale settings) in file names as \xxx, where xxx is the numeric value of the character in octal. -b As -B, but use C escape codes whenever possible. -C Force multi-column output; this is the default when output is to a terminal. -c Use time when file status was last changed for sorting (-t) or long printing (-l). ... code The **man** reader is essentially **less**, so you already know how to move up and down, and page by page!

Text Editors
Lastly, now that we can see into files, it would be nice to be able to create and edit our own files. We'll briefly describe the one of the two most common UNIX text editors, **vi**.

To open **vi**, we just issue the command at the prompt.

$ **vi**

First, the most elusive **vi** knowledge: how to exit **vi**.

First type a colon, then the letter q, and press enter.

Voila. The most unintuitive part is over.

To open a file in a new **vi** session, you can just add the filename to the command.

$ **vi myCombinedFile**

To edit a file with **vi**, you must first enter **insert mode**, which you do by typing the letter **i**.

Enter some text at the beginning of our file, and noticed that you can move up, down, left, and right with the arrow keys.

Now, press **Esc**, and we will return to **view mode**, which is how we began our **vi** session.

To write our changes to the file, we again enter a colon, this time following by a **w**, and then the **Return** key.

There are a great number of shortcuts and tricks to **vi**, and you can literally read a book on them. However, in the short term, you may be best served by simply googling for the **vi** command you don't know.

**Exercises**

 * 1) Cerevisiae chromosomes**

a) Change into your **fasta_files** directory, and unzip the remainder of the fasta files using only a one-line command.

b) Combine the sequence files to make a single whole genome file called "cerevisiae_genome.fasta"

d) Count the chromosomes in the whole genome file using commands from the lecture. (HINT: Each of the original FASTA files contains a single chromosome).

e) Look up the command **wc** and find out what it does. Get size of total genome. (HINT: The size of the genome can be determined by counting the number of bases).


 * 2) Cerevisiae genomic features**

a) Get the list of cerevisiae chromosome features from this address:

http://gonzo.qb3.berkeley.edu/~matt/SGD_features.tab

What does the -O flag for **wget** do?

Columns within SGD_features.tab:

1. Primary Stanford Gene Database ID (SGDID) (mandatory) 2. Feature type (mandatory) 3. Feature qualifier (optional) 4. Feature name (optional) 5. Standard gene name (optional) 6. Alias (optional, multiples separated by |) 7. Parent feature name (optional) 8. Secondary SGDID (optional, multiples separated by |) 9. Chromosome (optional) 10. Start_coordinate (optional) 11. Stop_coordinate (optional) 12. Strand (optional) 13. Genetic position (optional) 14. Coordinate version (optional) 15. Sequence version (optional) 16. Description (optional)

b) Next, count the total number of ORFs in the features file.

c) Now count the ORFs listed as Verified, and separately count those listed as Dubious. If you do the math and add up these two groups, why don't they make up all the ORF matches from **grep**?

d) Use the **cut** utility with **grep** to count the number of ORFs more accurately.

e) Use a combination of the the commands **cut, sort,** and **uniq** generate a list of all the genomic features (column 2) in this file. Don't forget that you can use the **man** pages to learn how to use new tools.


 * 3) Moving beyond the lecture**

a) Use google and any other references you want to find a command that tells you how much disk space you have left.

b) Use the **man** command to see how it works.

c) How much space is left on your system? Make the command output in terms of gigabytes and megabytes (a.k.a. the human readable form).


 * 4) Practice with the vi text editor**

a) Play around with the **vi** editor. Type your name on the first line and save the file as "myPracticeFile" What happens when you type a capital 'A' ? What about a capital 'I' ?

b) Cut and paste your name such that there are 4 lines with your name in the file (hint: the command to cut a line is typing a lowercase 'd' twice).

c) Save your file to a new name "myNewPracticeFile" and exit the editor.

Solutions