Session+1.1

=First Morning, Introductions, and Lesson Plans=

Your instructors are: Peter Combs, Aisha Ellahi, Diana Koulechova, Mike Lawson, and Josh Schraiber.

Your teaching assistants for the first week are: Justin Bosch, Ben Peter, Debbie Thurtle, and Mel Yang For the second week we have: Aaron Hardin, Ben Peter, Courtney French, and Jeremy Roop

Topics:

 * Expectations for the course
 * Navigating the UNIX shell
 * Viewing the content of files
 * How to get help
 * Text editors

Introduction
Welcome to the QB3 Introduction to Programming for Bioinformatics bootcamp!

Overview for today: 1) What should you expect to learn from this course. 2) What we are not going to cover. 3) How the class will be organized, including the instructors and TAs. 4) Learn a little about how to function in a UNIX environment.

What are you going to learn?
You are going to learn python :O)

Python is a simple and powerful programming language that is used for many applications from simple tasks to large software development projects. It has become popular as both a first language for beginning students and an everyday one for advanced programmers. Python is used by a range of companies including YouTube, Google, and Industrial Light and Magic.

Our goal is to allow you to apply programming to the problems that you face in the lab. Although we will only directly cover a couple application areas of programming to biology, we expect you to leave this course with a sufficiently generalized knowledge of programming that you will be able to apply your skills to whatever you happen to be working on.

What are you not going to learn?
__Issue 1__: Learning to program is a lot like learning a new language. It requires adjusting the way you think about solving a problem and communicating that solution. Even more confusing, each programmer develops his/her own style (accent). In practice, this means that there is almost never a "RIGHT ANSWER," but rather that there are almost infinite ways to solve almost any problem. In the course of the class, you will be exposed to several styles and see several ways to get to more complicated solutions. The goal, though, is to give you the tools to begin to develop a style of your own. Later on, you may also want to read PEP 8, which is a [|style guide for Python], much like the vaunted Strunk and White is a style guide for English.

__Issue 2__: Python is big. Thousands of computer scientists and programmers have used it, contributed to it, and extended it to their own sub-fields. And they keep improving, and thus changing it! We can't get to all of it, even if we had much longer than two weeks. Included in the list of subjects we will not cover is object-oriented programming, writing parallel programs, integrating your code with faster code written in C or C++, or a host of other powerful-but-subtle methods and topics. We will teach you enough that you should be able to go learn about them if and when you want.

__Issue 3:__ Python is evolving. At the moment, there are two major versions of Python available: Python 2.7 and Python 3.2. In this course, we'll be using Python 2.7. Why aren't we using the more up-to-date Python 3? There's a bit of history: For most of Python's lifetime, each new version of the language would introduce new features, but would try very, very hard to not break any code that other people had already written; in other words, most changes were backwards compatible. In about 2006, however, Python's creator and "Benevolent Dictator For Life" Guido van Rossum decided that there were a number of things that he had gotten wrong in the original Python specification, and would like to change. Making those changes //would// break other people's code, so it was decided to make them all at once. Although that version was released almost 4 years ago, there are lots of other libraries that haven't completely switched. The number of "gotchas" between Python 2 and 3 is relatively small, and we'll try to point out where there are differences, so if you do decide to make the leap, things should go relatively smoothly.

How are you going to learn it?
The course is broadly divided into two parts.

Week 1: Learning Python Basics

In the first week of the course we will learn the very basics of programming practice and the fundamentals of Python syntax, including:

- how to get information from files - how to store information - how to do interesting things with the information - how to print information back out - how to do really complicated things with the information - how to incorporate other people's code to do more faster, with less effort

Week 2: Python Applied to Bioinformatics

In the second week, we will use real data from several published studies on high-throughput sequencing for a range of biological applications. The second week will show us:

- how to build and manage a data analysis pipeline - how to call other programs from within our Python code - how to perform complicated scientific data analysis - how to visualize our data - a selection of other people's code that we find is particularly useful for biologists

Our daily schedule will generally proceed like this:

Start at 8:30 am 1-2 hour lecture 2-3 hours lab for exercises

Lunch from 12:30 - 1

1-2 hour lecture 2-3 hours lab for exercises Leave at 5 pm

You will have a number of exercises each day covering the breadth of the lectures. You will not be graded on these but it's REALLY important for you to be able to demonstrate what you've just learned. Just like learning French, one learns programming by doing. If you only finish half the problems, you've only really learned half the material.

Coding has a steep learning curve!
Learning to program is really HARD! REALLY! Don't worry if you get frustrated. Try to remember that python is a logic-based language and that you can reason your way around most problems we will be posing in the next two weeks. Ask questions! The idea is to get you to the point of being able to solve real problems in lab and to give you some tools to learn more on your own.

You have two incredibly useful resources at your disposal during the labs: first, you have us, the TAs and instructors, who are all familiar with the language and here to help you out. Second, you have the extensive documentation about python and programming that we will be introducing you to in the course of the class.

You can also access some resources here: Learning Python Python Pocket Reference Python Website (documentation) Linux Pocket Guide

Questions?

Using the UNIX shell
You will spend nearly all of your time in one of three places: the shell, the text editor, or the interactive interpreter. The shell allows you to move and copy files, run programs, and more, while the text editor is where you will write your programs. We will focus mostly on the shell this morning, although we will touch on the basic usage of a popular text editor, **emacs**. We will begin Python this afternoon. We'll cover the interactive interpreter, which is another powerful tool, later on in the course.

A large majority of what you can do in the shell (sometimes also called the "command line") can be done using the windowed operating system you're used to. While for the simplest of tasks, the command line may seem like a step backwards, for anything even mildly more complicated, it can save a lot of time.

Informative Interlude: Some notes on the formatting of the lessons for this course
Periodically in these lessons, 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.

Finally, when we use actual python code examples, they will be contained in the shaded boxes, such as:

code format="python" This is where code will appear. code

You'll notice that some of the words are in different colors. These words mean special things in Python, and the wiki software understands that, and will color the code to make the structure more clear. Many editors also have a "syntax highlighting" feature.

This concludes our first informative interlude.

Let's start by opening a new terminal window...

How do I move around?
[where am I?] (Print Working Directory) Prints the directory in which you are at the current moment. If you create any files, they will appear in this spot. When you first open the terminal shell, you will be in your "home" directory.
 * pwd**

$ **pwd** ///Users/pacombs//

[move to a new directory] (Change Directory) Given a complete path, this command moves your "current location" to the specified directory.
 * cd**

$ **cd PythonCourse**

$ **pwd** ///Users/pacombs/PythonCourse//

To go up, use the command **cd ..**

$ **pwd** ///Users/pacombs//
 * $ cd ..**

An aside on directories... Directories in UNIX are set up the same way as your regular 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!

[lists contents of a directory] (LiSt) Shows the files and directories.
 * ls** directory_path

$ **cd School/MCB142** $ **ls** //2010 Notes on plagerism.docx//


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

[lists the long form of the directory entries' security permissions, owners of files, sizes, date created]
 * ls -l**

[lists the long form of the directory entries, but with the sizes in a human-readable format (i.e. MB and GB instead of the number of bytes)]
 * ls -lh**

[shows long listing, and sorts by modification time]
 * ls -lt**

[reverses the list]
 * ls -lr**

[list contents of the directory above]
 * ls ..**

$ **ls -ltr** //drwxr-xr-x 2 pacombs staff 68 Jul 14 14:34 2010/// //-rw-r--r--@ 1 pacombs staff 33502 Jul 14 14:35 Notes on plagerism.docx//

Making your mark...
If you cd without giving a directory name, it will take you to your home directory.
 * $ cd**

[Create a given directory] (MaKe DIRectory) Exactly what it says - let's you create new directories.
 * mkdir** directory_name


 * $ mkdir PythonCourse**
 * $ cd PythonCourse**
 * $ mkdir S1.1**
 * $ cd S1.1**


 * $ echo 'Hello World' > python_notes.txt**

$ **ls** //python_notes.txt//

$ **mkdir data** $ **ls** //data python_notes.txt//

[copy file or directory] (CoPy) Create a copy of the original file
 * cp** original_name copy_name

$ **echo 'To Do' > project_notes.txt** $ **ls** //project_notes.txt data// //python_notes.txt//

$ **cp project_notes.txt backup.txt** $ **ls** //backup.txt project_notes.txt data// //python_notes.txt//

[move files or directories] (MoVe) Rename a file or directory.
 * mv** source destination

$ **mv backup.txt project_notes.txt** $ **ls** //project_notes.txt data// //python_notes.txt//

Peeking inside files
[view contents of a file]
 * less** file_name


 * less** shows the contents of a file, and allows you to scroll and search the contents. However, **less** can only be used for simple text files, so you cannot reliably view contents of, say, MS Word documents with **less**.

$ **less pythons_of_the_world.txt** //Why hello there!// //How are you this morning?// //Look what I just found :O)// //The Pythonidae, commonly known simply as pythons, from the Greek word// //python, are a family of non-venomous snakes found in Africa, Asia// //and Australia. Among its members are some of the largest snakes in the// //world. Eight genera and 26 species are currently recognized.[2]// //Contents// //1 Geographic range// //2 Conservation// //3 Behavior// //4 Feeding/// /5 Reproduction 6 Captivity 7 Genera 8 Taxonomy 9 Gallery 10 See also//

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**.

Optional 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] ." Your teachers and TAs may use the **more** command interchangeable with **less** throughout the class.

[print first 10 lines of the file]
 * head** filename

By default, **head** prints the top 10 lines of the input file. To print a different number, say 12, lines: $ **head -n 12 filename** $ **head** **pythons_of_the_world.txt** //The Pythonidae, commonly known simply as pythons, from the Greek word python-πυθων, are a family of non-venomous snakes found in Africa, Asia and Australia. Among its members are some of the largest snakes in the world. Eight genera and 26 species are currently recognized.[2]// //Contents [hide]// //1 Geographic range// //2 Conservation// //3 Behavior// //4 Feeding// //5 Reproduction// //6 Captivity// //7 Genera// //8 Taxonomy//

[print the last ten lines of the file]
 * tail** filename

$ **tail** **pythons_of_the_world****.txt** //^ a b c d e McDiarmid RW, Campbell JA, Touré T. 1999. Snake Species of the World: A Taxonomic and Geographic Reference, vol. 1. Herpetologists' League. 511 pp. ISBN 1-893777-00-6 (series). ISBN 1-893777-01-4 (volume).// //^ a b c d e "Pythonidae". Integrated Taxonomic Information System. Retrieved 15 September 2007.// //^ Huge, Freed Pet Pythons Invade Florida Everglades at http://news.nationalgeographic.com/news/ National Geographic News. Accessed 16 September 2007.// //^ Hardy, David L. (1994). A re-evaluation of suffocation as the cause of death during constriction by snakes. Herpetological Review 229: 45-47.// //^ Mehrtens JM. 1987. Living Snakes of the World in Color. New York: Sterling Publishers. 480 pp. ISBN 0-8069-6460-X.// //^ Stidworthy J. 1974. Snakes of the World. Grosset & Dunlap Inc. 160 pp. ISBN 0-448-11856-4.// //^ Carr A. 1963. The Reptiles. Life Nature Library. Time-Life Books, New York. 192 pp. LCCCN 63-12781.// //^ The Keeping of Large Pythons at Anapsid. Accessed 16 September 2007.// //[edit]//

[print named files to the screen] (conCATenate) If given just one file, **cat** will print the contents of the file to the screen. Given multiple files, it will print one after another.
 * cat** file1 file2 ...

$ **cat cat1.txt** //HEY EVERYONE!!!// $ **cat cat2.txt** //WISH I WAS OUTSIDE PLAYING :O(// $ **cat cat1.txt cat2.txt** //HEY EVERYONE!!!// //WISH I WAS OUTSIDE PLAYING :O(//

(Global Regular Expression Print) Searches for the "search string" in a text file and prints out all lines where it find the desired text. The search string can be a simple word, or a complicated specification of matches/mismatches.
 * grep** 'search_string' file1 [file2 ...]

$ **grep python pythons_of_the_world.txt** //The Pythonidae, commonly known simply as pythons, from the Greek word python (πυθων), are a family of nonvenomous snakes found in Africa, Asia and Australia. Among its members are some of the largest snakes in the world. Eight genera and 26 species are currently recognized.[2]// //In the United States, an introduced population of Burmese pythons, Python molurus bivittatus, has existed as an invasive species in the Everglades National Park since the late 1990s.[3]// //Many species have been hunted aggressively, which has decimated some, such as the Indian python, Python molurus.// //Black-headed python,// //Larger specimens usually eat animals about the size of a house cat, but larger food items are known: some large Asian species have been known to take down adult deer, and the African rock python, Python sebae, has been known to eat antelope. Prey is swallowed whole, and may take anywhere from several days or even weeks to fully digest.// //Contrary to popular belief, even the larger species, such as the reticulated python, P. reticulatus, do not crush their prey to death; in fact, prey is not even noticeably deformed before it is swallowed. The speed with which the coils are applied is impressive and the force they exert may be significant, but death is caused by suffocation, with the victim not being able to move its ribs to breathe while it is being constricted.[5][6][7]// //Apodora Kluge, 1993 1 0 Papuan python Most of New Guinea, from Misool to Fergusson Island// //Bothrochilus Fitzinger, 1843 1 0 Bismark ringed python The islands of the Bismark Archipelago, including Umboi, New Britain, Gasmata (off the southern coast), Duke of York and nearby Mioko, New Ireland and nearby Tatau (off the east coast), the New Hanover Islands and Nissan Island// //Leiopython Hubrecht, 1879 1 0 D'Albert's water python Most of New Guinea (below 1200 m), including the islands of Salawati and Biak, Normanby, Mussau, as well as a few islands in the Torres Strait// //Carpet python,// //Green tree python,// //Albino Burmese python,// //Borneo short-tailed python,//

The **-c** argument counts the number of lines (not the number of matches).

$ **grep -c python pythons_of_the_world.txt** //13//

The **-v** argument inVerts the search (i.e. prints lines that *don't* contain your search string).


 * cut -f** column_number(s) file

Many of the data files we'll be dealing with are actually tables, usually separated by tabs. The cut command will pull out the column numbers you specify and print them out to the shell, while leaving the original file alone.

wildcard matching with the *
The star functions as a "wild-card" character that matches any non-specified characters.

$ **ls** //cat1.txt cat2.txt chimera pythons_of_the_world.txt// $ **ls *.txt** //cat1.txt cat2.txt linux_text.txt//

The star can go anywhere in a list of arguments you're supplying, even in the middle of words!

pipe |
(the one above the backslash "\" key)

Piping with **|** connects UNIX commands, allowing the output of one command to "flow through the pipe" to another.

$ **env** //TERM_PROGRAM=iTerm.app// //GPG_AGENT_INFO=/Users/pcombs/.gnupg/S.gpg-agent:330:1// //TERM=xterm// //SHELL=/bin/bash// //TMPDIR=/var/folders/bc/d77vgvv951l46q9xwg0hcv7m0000gn/T/// //Apple_PubSub_Socket_Render=/tmp/launch-0IvbkX/Render// //FORTUNE_FILE=/Users/pcombs/fortunes/fortunes// //LC_ALL=C// //USER=pacombs// //COMMAND_MODE=unix2003// //SSH_AUTH_SOCK=/tmp/launch-0sJG9c/Listeners// //__CF_USER_TEXT_ENCODING=0x1F5:0:0// //Apple_Ubiquity_Message=/tmp/launch-Qdbc5M/Apple_Ubiquity_Message// //ECHO_NEST_API_KEY=HDSBAQR2XXGS4XMMN// //NLTK_DATA=/usr/share/nltk// //MKL_NUM_THREADS=1// //PWD=/Users/pcombs// //EDITOR=vim// //LANG=en_US.UTF-8// //ITERM_PROFILE=default// //PS1=\[\033[0;34m\][\h:\W\[\033[1;34m\]$(parse_git_branch)\[\033[0;34m\]]\[\e[m\] $// //MAGICK_HOME=/Users/pcombs/ImageMagick-6.7.2// //PS2=>// //SHLVL=1// //HOME=/Users/pcombs// //DYLD_LIBRARY_PATH=/Users/pcombs/ImageMagick-6.7.2/lib/// //ITERM_SESSION_ID=w0t1p0// //LOGNAME=pacombs// //PROMPT_COMMAND=: && { (autojump -a "$(pwd -P)"&)>/dev/null 2>>${HOME}/.autojump_errors;} 2>/dev/null// //DISPLAY=/tmp/launch-kDhQ3q/org.x:0// //GL_ENABLE_DEBUG_ATTACH=YES// //SECURITYSESSIONID=186a8// //_=/usr/bin/env//

$ **env | head** //TERM_PROGRAM=iTerm.app// //GPG_AGENT_INFO=/Users/pcombs/.gnupg/S.gpg-agent:330:1// //TERM=xterm// //SHELL=/bin/bash// //TMPDIR=/var/folders/bc/d77vgvv951l46q9xwg0hcv7m0000gn/T/// //Apple_PubSub_Socket_Render=/tmp/launch-0IvbkX/Render// //FORTUNE_FILE=/Users/pcombs/fortunes/fortunes// //LC_ALL=C// //USER=pacombs//

COMMAND_MODE=unix2003 $ **env | grep home** //HOME=/Users/pacombs//

**Redirection** with **>**
In addition to redirecting output to another command, the results can be sent into a file with the **>**

$ **cat cat1.txt cat2.txt > wishes.txt** $ **cat wishes.txt** //HEY EVERYONE!!!////WISH I WAS OUTSIDE PLAYING :O(//

Permissions
Unlike the computers you are used to, UNIX doesn't automatically know what to do with files (e.g. It won't know to use Word to open a .doc document).

The first thing that controls a file is the file's permissions. You can control who can read, write, and execute (run as a program) each of your files.

$ **ls -la** //drwxr-xr-x 6 aaron staff 204 Jul 14 22:20 ./// //drwxr-xr-x 8 aaron staff 272 Jul 14 14:17 ../// //-rw-r--r-- 1 aaron staff 4 Jul 14 22:20 cat1.txt// //-rw-r--r-- 1 aaron staff 5 Jul 14 22:20 cat2.txt// //-rw-r--r-- 1 aaron staff 3624 Jul 14 17:26 pythons_of_the_world.txt// //-rw-r--r-- 1 aaron staff 9 Jul 14 22:20 wishes.txt//

The first letter tells you whether it is a directory.

The next set of letters tell you if a file is readable (r), writable (w), or executable (x).

The 2nd-4th letters tell you what *your* permissions are, 5th-7th tell you what your group's permissions are, and the last three tell you what the rest of the world's permissions are. Unix was designed to be a multi-user operating system, so even if you're the only one who uses the computer, it maintains the distinction for you, versus your group, versus everyone else.

Modify permissions.
 * chmod** [flags] [filename]

$ **ls -l script.py** //-rw-r--r-- 1 aaron staff 0 Jul 14 22:21 script.py// $ **chmod +x script.py****t** //chmod: cannot access `script.pyt': No such file or directory// $ **chmod +x script.py** //-rwxr-xr-x 1 aaron staff 0 Jul 14 22:21 script.py//
 * $ ls -l script.py**

Aisha is going to explain how to get UNIX to run your executable scripts this afternoon. However, if you try running a program and it's not working at some point in the class, double check the permissions!!!

Help, I'm stuck!
[what does that command do again?]
 * man** command_name

Most commands have many useful flags beyond what I've shown you. For information on a particular command, look at the MANual pages with **man**. code $ **man chmod** CHMOD(1)                 BSD General Commands Manual                 CHMOD(1)

NAME chmod -- change file modes or Access Control Lists

SYNOPSIS chmod [-fv] [-R [-H | -L | -P]] mode file ...    chmod [-fv] [-R [-H | -L | -P]] [-a | +a | =a] ACE file ...     chmod [-fhv] [-R [-H | -L | -P]] [-E] file ...     chmod [-fhv] [-R [-H | -L | -P]] [-C] file ...     chmod [-fhv] [-R [-H | -L | -P]] [-N] file ...

DESCRIPTION The chmod utility modifies the file mode bits of the listed files as    specified by the mode operand. It may also be used to modify the Access Control Lists (ACLs) associated with the listed files.

The generic options are as follows:

-f     Do not display a diagnostic message if chmod could not modify the mode for file.

-H     If the -R option is specified, symbolic links on the command line are followed. (Symbolic links encountered in the tree traversal            are not followed by default.)

-h     If the file is a symbolic link, change the mode of the link itself rather than the file that the link points to.

-L     If the -R option is specified, all symbolic links are followed.

-P     If the -R option is specified, no symbolic links are followed. This is the default.

-R     Change the modes of the file hierarchies rooted in the files instead of just the files themselves.

-v     Cause chmod to be verbose, showing filenames as the mode is modi- fied. If the -v flag is specified more than once, the old and new modes of the file will also be printed, in both octal and symbolic notation.

The -H, -L and -P options are ignored unless the -R option is specified. In addition, these options override each other and the command's actions are determined by the last one specified.

Only the owner of a file or the super-user is permitted to change the mode of a file. ... code

Text Editors
Lastly, now that we can see into files, it would be nice to be able to create and edit our own files. And... our first lesson in programming accents: different programmers use different text editors. I am going to introduce three common options here. Each has pluses and minuses depending on your needs. There is no 'right' one, so play around and pick your fav. Note that each of the teachers will be using their fav, so don't worry if they are using something different than you. These can all operate in the terminal window, and for some quick edits, it may make sense to do it that way, although they also have standalone programs. Often, you'll want to have that window open editing your code, save, jump over to the terminal, and then run your code.

Program 1: vi open a file: vi [filename] write to file: i save a file: :w close: :q

Vi is somewhat unique in that it has a couple major "modes". The default, "normal mode" is not actually the one where you write text, so you need to use i to go into "insert mode", then ESC to get back to normal mode, where you can save, search, etc.

Program 2: emacs open a file: emacs [filename] save a file: CTRL-X CTRL-S close: CTRL-X CTRL-C

Emacs (including Aquamacs) has many, many short-cut keys or "accelerators." A quick Googling of "Emacs Cheat Sheet" will reveal several resources, such as this one from the Princeton CS department: [|Emacs Cheat Sheet]

Program 3: nedit (gedit) open a file: nedit [filename] save a file: CTRL-S close a file: CTRL-C pulldown menu!!!

Questions?

**Exercises**

 * 1) Cerevisiae chromosomes**

a) In your top-level directory, make a new directory called "fasta_files" and change into it b) Go to http://downloads.yeastgenome.org/sequence/S288C_reference/chromosomes/fasta/ and individually download each of the files ending in **.fsa**. These are the chromosomes of the yeast, //S. cerevisiae//. You may have to right-click these files depending on your web browser (and be aware, some browsers will save your file with a **.txt** extenstion). c) 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 characters not on the same line as a fasta header).


 * 2) Cerevisiae genes**

a) Get the list of cerevisiae chromosome features: @http://downloads.yeastgenome.org/curation/chromosomal_feature/SGD_features.tab code Columns within SGD_features.tab:

1.  Primary Standfor 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)

code

b) Count total genes c) Count only verified genes. Count only uncharacterized genes. d) What other types of genes are in this file? For this, you may want to use the **sort** command with the **-u** flag, which will sort the input alphabetically, then take only unique lines.

From the same directory as your fasta files, see if you can predict what each of these commands will do (then try it) a) head * b) head *.fsa c) head chr1*.fsa d) head chr1* e) head chr*1.fsa f) head chr*1 g) grep 'S288C' * h) grep 'S288C' *.fsa i) grep 'BK006935.2' * j) cat * | grep 'BK006935.2' (what's the difference in the output between this one and the last one?) k) head *.fsa | grep 'chr' l) head *.fsa | grep 'chromosome' (what's the difference in the output between this one and the last one?)
 * 3) Star-struck**

a) Using the command line, copy the files "palinsreg" and "palinscmp" from the provided "data" directory to today's directory (S1.1). These are detected terminator sequences in the //E. coli// genome (using the program [|GeSTer], if you're curious). b) The command **grep '/G=[^ ]*' somefile** will find all lines that match /G=//somegenename//, where somegenename is a sequence of non-blank characters. Read the output of **man grep** and figure out how to //-o//nly print /G=//somegenename//, rather than the whole line. c) Pipe the results of part b) through a **cut** command to get only everything after the = d) Store the results of part c) in a file named "terminated_genes.txt' e) BONUS: google for a Unix command that only keeps each gene once, rather than once per annotated terminator.
 * 4) Building a pipeline**

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-- 'human-readable' form.
 * 5) Moving beyond the lecture**

a) Play around with the three text editors I just introduced. b) Using your favorite editor, write a short note about what you are most excited about learning in this class. Email it to us at intro.prog.bioinformatics@gmail.com.
 * 6) Picking your favorite text editor**

Solutions
1) Cerevisiae Chromosomes a, b) Just do it! c) $ **cat *.fsa > cerevisiae_genome.fasta** d) $ **grep -c '>' cerevisiae_genome.fasta** e) $ grep -v '>' cerevisiae_genome.fasta | wc //202628 202628 12359733// Then, subtract 202628 (the number of "newline" characters) from 12 359 733. In short, still about 12 megabases.

2) Cerevisiae Genes a) Do it! b) $ **grep -c CDS SGD_features.tab** //7078// c) $ **grep ORF SGD_features.tab | grep Verified | wc -l** //4974//

$ **grep ORF SGD_features.tab | grep Uncharacterized | wc -l** //848//

d) $ **cut -f 3 SGD_features.tab | sort -u**

//Dubious// //Uncharacterized// //Verified// //Verified|silenced_gene// //silenced_gene//

3) Star-struck a) This prints the first 10 lines of every file in the directory b) This prints the first 10 lines of every file in the directory that ends with .fsa (but not .fasta) c, d) The first 10 lines of every file in the directory where the filename starts with chr1 (i.e. chr10.fsa, chr11.fsa, etc) e) The first 10 lines of chr01.fsa and chr11.fsa f) Nothing! There is no file that starts with chr and ends with 1 g, h) Note again that cerevisiae_chromosome.fasta does not end with .fsa! i, j) cerevisiae_genome.fasta: //>tpg|BK006935.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=I] [note=R64-1-1]// chr01.fsa: //>tpg|BK006935.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=I] [note=R64-1-1]// //>tpg|BK006935.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=I] [note=R64-1-1]// //>tpg|BK006935.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=I] [note=R64-1-1]//
 * $ grep 'BK006935.2'** *
 * $ cat * | grep 'BK006935.2'**

Note that the first one, grep will put the name of the file it found it in at the beginning of the line, whereas in the second, once they've ben cat'ed together, the filename goes away.

k, l) //==> chr01.fsa <==// //>tpg|BK006935.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=I] [note=R64-1-1]// //==> chr02.fsa <==// //>tpg|BK006936.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=II] [note=R64-1-1]// //==> chr03.fsa <==// //>tpg|BK006937.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=III] [note=R64-1-1]// //==> chr04.fsa <==// //>tpg|BK006938.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=IV] [note=R64-1-1]// //==> chr05.fsa <==// //>tpg|BK006939.2| [organism=Saccharomyces cerevisiae S288c] [strain=S288c] [moltype=genomic] [chromosome=V] [note=R64-1-1]//

//...//

Note that when you do **head** on multiple files, it includes the name of each file in ==> <==. When grep'ing for chr, you find the chr in the name of the file, as well as the chr inside the file, whereas chromosome only matches inside the file.

4) Building a Pipeline a) something like: $ **cp Downloads/palins* PythonCourse/S1.1** works b) $ **grep -o '/G=[^ ]*' palins*** c) $ **grep -o '/G=[^ ]*' palins* | cut -d '=' -f 2** d) $ **grep -o '/G=[^ ]*' palins* | cut -d '=' -f 2 > terminated_genes.txt** e) $ **grep -o '/G=[^ ]*' palins* | cut -d '=' -f 2 | sort -u > terminated_genes.txt**

5) Moving beyond the lecture Like Debbie said, google is your friend. I searched for "unix disk space" and clicked on the first result...

$ df -h