ELA_07_Basic_Skills

Scope of this Manual

This manual provides a brief introduction how to get started using powerful Linux command-line utilities.

How to Get Access?

Install your preferred GNU/Linux distribution on your local machine (not required!!!)

Users at UC Riverside can apply for an account on our Linux clusters by sending an account request to Thomas Girke (tgirke@citrus.ucr.edu).

Logging-In Mac or LINUX

To log-in into the remote Linux shell, open terminal and type:

ssh -X <your_username>@<host_name>

host name is the remote server's domain name (e.g. biocluster.ucr.edu)
You will be asked to enter the password, simply type it and press enter.

To copy files To the server run the following on your workstation or laptop:

scp -r <path_to_directory> <your_username>@<host_name>:

To copy files From the server run the following on your workstation or laptop:

scp -r <your_username>@<host_name>:<path_to_directory> .

Setup for graphics emulation. Download and install Xming if you do not have it.

Use WinSCP or FileZilla for file exchange. Download and install WinSCP or FileZilla if you do not have it.

Why GNU/Linux?

Software costs $0

Advanced Multitasking

Remote tasking ("real networking")

Multiuser

Easy access to programming languages, databases, open-source projects

Software freedoms
0. Free to use for any purpose
1. Free to study and modify the source code
2. Free to share
3. Free to share modified versions

No dependence on vendors

Better performance

More up-to-date

Many more reasons ...

GNU/Linux Distributions

Ubuntu, Debian, CentOS, RedHat, Fedora, Slackware, SuSE, Darwin, and more...

Family tree of the GNU/Linux distributions

Basics

Command-Line Syntax for this Manual

Remember the UNIX/LINUX command line is case sensitive!

All commands in this manual are printed in gray code boxes.

Commands given in red are considered more important for beginners than commands given in black.

The hash (pound) sign "#" indicates end of a command and the start of a comment.

The notation <...> refers to variables and file names that need to be specified by the user. The symbols < and > need to be excluded.

Orientation

Viewing and changing the present working directory:

pwd # Get full path of the present working directory (same as "echo $HOME")

ls # Content of pwd
ls -l # Similar as ls, but provides additional info on files and directories
ls -a # Includes hidden files (.name) as well
ls -R # Lists subdirectories recursively
ls -t # Lists files in chronological order

cd <dir_name> # Switches into specified directory.
cd # Brings you to the highest level of your home directory.
cd .. # Moves one directory up
cd ../../ # Moves two directories up (and so on)
cd - # Go back to you were previously (before the last directory change)

The tilde symbol (~) gets interpreted as the path to your home directory. This will happen anywhere on the command line:

echo ~ # View the full (complete) path of your home
find ~ # List all your files (including everything in sub-directories)
ls ~ # List the top level files of your home directory
du -sch ~/* # Calculate the file sizes in your home

Viewing file info, user, and host:

stat <file-name> # Last modification time stamps, permissions, and size of a file

whoami # Shows your user name (same as "echo $USER")
hostname # Shows on which machine you are (same as "echo $HOSTNAME")

Files and directories

mkdir <dir_name> # Creates specified directory
rmdir <dir_name> # Removes empty directory
rm <file_name> # Removes file name
rm -r <dir_name> # Removes directory including its content, but asks for confirmation,
# 'f' argument turns confirmation off
cp <name> <path> # Copy file/directory as specified in path (-r to include content in directories)
mv <name1> <name2> # Renames directories or files
mv <name> <path> # Moves file/directory as specified in path

Copy and paste

The methods differ depending where you are.

In a command line environment:

Cut last word with keyboard only

Ctrl+w

Press multiple times to cut more than one word

Paste with keyboard only

Ctrl+y

In a non-command line desktop environment:

Copy

Ctrl+c

Paste

Ctrl+v

Command line <-> desktop exchange:

Copy text out of the command line and into the desktop:

Shift+Ctrl+c or Apple+c

Paste text from the desktop into the command line:

Shift+Ctrl+v or Apple+v

On any Linux desktop!

Copy with mouse only

Simply select the text with the mouse

Paste with mouse only

Click the middle mouse button or both left/right buttons simultaneously

Handy shortcuts

Anywhere in Command Line:

up(down)_key - scrolls through command history

history # shows all commands you have used recently

Auto Completion:

<something-incomplete> TAB - completes program_path/file_name

Taking control over the cursor (the pointer on the command line):

Ctrl+a # cursor to beginning of command line
Ctrl+e # cursor to end of command line
Ctrl-w # Cut last word
Ctrl+k # cut to the end of the line
Ctrl+y # paste content that was cut earlier (by Ctrl-w or Ctrl-k)

When specifying file names:

"." (dot) - refers to the present working directory

"~" (Tilda) or "~/" - refers to user's home directory

Unix Help

man <something> # general help (press the 'q' key to exit)
man wc # manual on program 'word count' wc
wc --help # short help on wc

soap -h # for less standard programs

Online help: Google

Universally available Linux commands, with detailed examples and explanations: http://www.linuxconfig.org/linux-commands

Finding Things

Finding files, directories and applications

find -name "*pattern*" # searches for *pattern* in and below current directory
find /usr/local -name "*blast*" # finds file names *blast* in specfied directory
find /usr/local -iname "*blast*" # same as above, but case insensitive

additional useful arguments: -user <user name>, -group <group name>, -ctime <number of days ago changed>

find ~ -type f -mtime -2 # finds all files you have modified in the last two days
locate <pattern> # finds files and dirs that are written into update file
which <application_name> # location of application
whereis <application_name> # searches for executeables in set of directories
dpkg -l | grep mypattern # find Debian packages and refine search with grep pattern

Finding things in files

grep pattern file # provides lines in 'file' where pattern 'appears',
# if pattern is shell function use single-quotes: '>'


grep -H pattern # -H prints out file name in front of pattern
grep 'pattern' file | wc # pipes lines with pattern into word count wc
# wc arguments: -c: show only bytes, -w: show only words,
# -l: show only lines; help on regular expressions:
# $ man 7 regex or man perlre


find /home/my_dir -name '*.txt' | xargs grep -c ^.* # counts line numbers on many
# files and records each count along with individual file
# name; find and xargs are used to circumvent the Linux
# wildcard limit to apply this function on thousands of files.

Permissions and Ownership

List directories and files

$ ls -al # shows something like this for each file/dir: drwxrwxrwx
# d: directory
# rwx: read write execute
# first triplet: user permissions (u)
# second triplet: group permissions (g)
# third triplet: world permissions (o)

Assign write and execute permissions to user and group

chmod ug+rx my_file

To remove all permissions from all three user groups

chmod ugo-rwx my_file
# '+' causes the permissions selected to be added
# '-' causes them to be removed
# '=' causes them to be the only permissions that the file has.

chmod +rx public_html/ or $ chmod 755 public_html/ # Example for number system:

Change ownership

chown <user> <file or dir> # changes user ownership
chgrp <group> <file or dir> # changes group ownership
chown <user>:<group> <file or dir> # changes user & group ownership

Useful Unix Commands

df # disk space
free -g # memory info in Megabytes
uname -a # shows tech info about machine
bc # command-line calculator (to exit type 'quit')
wget ftp://ftp.ncbi.nih.... # file download from web
/sbin/ifconfig # give IP and other network info
ln -s original_filename new_filename # creates symbolic link to file or directory
du -sh # displays disk space usage of current directory
du -sh * # displays disk space usage of individual files/directories
du -s * | sort -nr # shows disk space used by different directories/files sorted by size

Process Management

General

top # view top consumers of memory and CPU (press 1 to see per-CPU statistics)
who # Shows who is logged into system
w # Shows which users are logged into system and what they are doing
ps # Shows processes running by user
ps -e # Shows all processes on system; try also '-a' and '-x' arguments
ps aux | grep <user_name> # Shows all processes of one user
ps ax --tree # Shows the child-parent hierarchy of all processes
ps -o %t -p <pid> # Shows how long a particular process was running.
# (E.g. 6-04:30:50 means 6 days 4 hours ...)
Ctrl z <enter> # Suspend (put to sleep) a process
fg # Resume (wake up) a suspended process and brings it into foreground
bg # Resume (wake up) a suspended process but keeps it running
# in the background.
Ctrl c # Kills the process that is currently running in the foreground
kill <process-ID> # Kills a specific process
kill -9 <process-ID> # NOTICE: "kill -9" is a very violent approach.
# It does not give the process any time to perform cleanup procedures.
kill -l # List all of the signals that can be sent to a proccess
kill -s SIGSTOP <process-ID> # Suspend (put to sleep) a specific process
kill -s SIGCONT <process-ID> # Resume (wake up) a specific process
renice -n <priority_value> # Changes the priority value, which range from 1-19,
# the higher the value the lower the priority, default is 10.

More on Terminating Processes

Terminating a Running Process

Text Viewing

more <my_file> # views text, use space bar to browse, hit 'q' to exit
less <my_file> # a more versatile text viewer than 'more', 'q' exits, 'G' moves to end of text, 'g' to beginning, '/' find forward, '?' find backwards
cat <my_file> # concatenates files and prints content to standard output

Text Editors

Vi and Vim

Non-graphical (terminal-based) editor. Vi is guaranteed to be available on any system. Vim is the improved version of vi.

Emacs

Non-graphical or window-based editor. You still need to know keystroke commands to use it. Installed on all Linux distributions and on most other Unix systems.

XEmacs

More sophisticated version of emacs, but usually not installed by default. All common commands are available from menus. Very powerful editor, with built-in syntax checking, Web-browsing, news-reading, manual-page browsing, etc.

Pico

Simple terminal-based editor available on most versions of Unix. Uses keystroke commands, but they are listed in logical fashion at bottom of screen.

Nano

A simple terminal-based editor which is default on modern Debian systems.

Vim Manual

Basics

vim my_file_name # open/create file with vim

Once you are in Vim the most important commands are i , : and ESC. The i key brings you into the insert mode for typing. The ESC brings you out of there. And the : key starts the command mode at the bottom of the screen. In the following text, all commands starting with : need to be typed in the command mode. All other commands are typed in the normal mode after hitting the ESC key.

Modifier Keys to Control Vim

i # INSERT MODE

ESC # NORMAL (NON-EDITING) MODE

: # commands start with ':'

:w # save command; if you are in editing mode you have to hit ESC first!!

:q # quit file, don't save

:q! # exits WITHOUT saving any changes you have made

:wq # save and quit

R # replace MODE

r # replace only one character under cursor

q: # history of commands (from NORMAL MODE!), to reexecute one of them, select and hit enter!

:w new_filename # saves into new file

:#,#w new_filename # saves specific lines (#,#) to new file

:# go to specified line number

Help

Online Help

Find help on the web. Google will find answers to most questions on vi and vim (try searching for both terms).

Purdue University Vi Tutorial

Animated Vim Tutorial: http://www.linuxconfig.org/Vim_Tutorial

Useful list of vim commands:

Vim Commands Cheat Sheet

VimCard

Vim Basics

Help from Command Line

vimtutor # open vim tutorial from shell

Help in Vim

:help # opens help within vim, hit :q to get back to your file

:help <topic> # opens help on specified topic

:help_topic| CTRL-] # when you are in help this command opens help topic specified between |...|, CTRL-t brings you back to last topic

$ :help <topic> CTRL-D # gives list of help topics that contain key word

$ : <up-down keys> # like in shell you get recent commands!!!!

Moving Around in Files

$ # moves cursor to end of line

A # same as $, but switches to insert mode

0 (zero) # moves cursor to beginning of line

CTRL-g # shows at status line filename and the line you are on

SHIFT-G # brings you to bottom of file, type line number (isn't displayed) then SHIFT-G # brings you to specified line#

Line Wrapping and Line Numbers

:set nowrap # no word wrapping, :set wrap # back to wrapping

:set number # shows line numbers, :set nonumber # back to no-number mode

Working with Many Files & Splitting Windows

vim -o *.txt # opens many files at once and displays them with horizontal
# split, '-O' does vertical split
vim *.txt # opens many files at once; ':n' switches between files

:wall or :qall # write or quit all open files

:args *.txt # places all the relevant files in the argument list

:all # splits all files in the argument list (buffer) horizontally

CTRL-w # switch between windows

:split # shows same file in two windows

:split <file-to-open> # opens second file in new window

:vsplit # splits windows vertically, very useful for tables, ":set scrollbind" let's you scroll all open windows simultaneously

:close # closes current window

:only # closes all windows except current one

Spell Checking & Dictionary

:set spell # turns on spell checking

:set nospell # turns spell checking off

:! dict <word> # meaning of word

:! wn 'word' -over # synonyms of word

Enabling Syntax Highlighting

:set filetype=perl # Turns on syntax coloring for a chosen programming language.

:set syntax on # Turns syntax highlighting on

:set syntax off # Turns syntax highlighting off

Undo and Redo

u # undo last command

U # undo all changes on current line

CTRL-R # redo one change which was undone

Deleting Things

x # deletes what is under cursor

dw # deletes from curser to end of word including the space

de # deletes from curser to end of word NOT including the space

cw # deletes rest of word and lets you then insert, hit ESC to continue with NORMAL mode

c$ # deletes rest of line and lets you then insert, hit ESC to continue with with NORMAL mode

d$ # deletes from cursor to the end of the line

dd # deletes entire line

2dd # deletes next two lines, continues: 3dd, 4dd and so on.

Copy & Paste

yy # copies line, for copying several lines do 2yy, 3yy and so on

p # pastes clipboard behind cursor

Search in Files

/my_pattern # searches for my_pattern downwards, type n for next match

?my_pattern # seraches for my_pattern upwards, type n for next match

:set ic # switches to ignore case search (case insensitive)

:set hls # switches to highlight search (highlights search hits)

Replacements with Regular Expression Support

Great intro: A Tao of Regular Expressions

:s/old_pat/new_pat/ # replaces first occurrence in a line

:s/old_pat/new_pat/g # replaces all occurrence in a line

:s/old_pat/new_pat/gc # add 'c' to ask for confirmation

:#,#s/old_pat/new_pat/g # replaces all occurrence between line numbers: #,#

:%s/old_pat/new_pat/g # replaces all occurrence in file

:%s/\(pattern1\)\(pattern2\)/\1test\2/g # regular expression to insert, you need here '\' in front of parentheses (<# Perl)

:%s/\(pattern.*\)/\1 my_tag/g # appends something to line containing pattern (<# .+ from Perl is .* in VIM)

:%s/\(pattern\)\(.*\)/\1/g # removes everything in lines after pattern

:%s/\(At\dg\d\d\d\d\d\.\d\)\(.*\)/\1\t\2/g # inserts tabs between At1g12345.1 and Description

:%s/\n/new_pattern/g #Replaces return signs

:%s/pattern/\r/g #Replace pattern with return signs!!

:%s/\(\n\)/\1\1/g # insert additional return signs

:%s/\(^At\dg\d\d\d\d\d.\d\t.\{-}\t.\{-}\t.\{-}\t.\{-}\t\).\{-}\t/\1/g # replaces content between 5th and 6th tab (5th column), '{-}' turns off 'greedy' behavior

:#,#s/\( \{-} \|\.\|\n\)/\1/g # performs simple word count in specified range of text

:%s/\(E\{6,\}\)/<font color="green">\1<\/font>/g # highlight pattern in html colors, here highlighting of >= 6 occurences of Es

:%s/\([A-Z]\)/\l\1/g # change uppercase to lowercase, '%s/\([A-Z]\)/\u\1/g' does the opposite

:g/my_pattern/ s/\([A-Z]\)/\l\1/g | copy $ # uses 'global' command to apply replace function only on those lines that match a certain pattern. The 'copy $' command after the pipe '|' prints all matching lines at the end of the file.

:args *.txt | all | argdo %s/\old_pat/new_pat/ge | update # Command 'args' places all relevant files in the argument list (buffer); 'all' displays each file in separate split window; command 'argdo' applies replacement to all files in argument list (buffer); flag 'e' is necessary to avoid stop at error messages for files with no matches; command 'update' saves all changes to files that were updated.

Useful Utilities in Vim

Matching Parentheses

Place curser on (, [ or { and type % # curser moves to matching parentheses

Printing and Inserting Files

:ha # prints entire file

:#,#ha # prints specified lines: #,#

:r <filename> # inserts content of specified file after cursor

Convert Text File to HTML Format

:runtime! syntax/2html.vim # run this command with open file in Vim

Shell Commands in Vim

:!<SHELL_COMMAND> <ENTER> # executes any shell command, hit <enter> to return

:sh # switches window to shell, 'exit' switches back to vim

Using Vim as Table Editor

v # starts visual mode for selecting characters

V # starts visual mode for selecting lines

CTRL-V # starts visual mode for selecting blocks (use CTRL-q in gVim under Windows). This allows column-wise selections and operations like inserting and deleting columns. To restrict substitude commands to a column, one can select it and switch to the command-line by typing ':'. After this the substitution sytax for a selected block looks like this: '<,'>s///.

:set scrollbind # starts simultaneous scrolling of 'vsplitted' files. To set to horizontal binding of files, use command ':set scrollopt=hor' (after first one). Run all these commands before the ':split' command.

:AlignCtrl I= \t then :%Align # This allows to align tables by column separators (here '\t') when the Align utility from Charles Campbell's is installed. To sort table rows by selected lines or block, perform the visual select and then hit F3 key. The rest is interactive. To enable this function, one has to include in the .vimrc file the Vim sort script from Gerald Lai.

Modify Vim Settings

The default settings in Vim are controlled by the .vimrc file in your home directory.

see last chapter of vimtutor (start from shell)

useful .vimrc sample

when vim starts to respond very slowly then one may need to delete the .viminf* files in home directory

The Unix Shell

When you log into UNIX/LINUX system, then is starts a program called the Shell. It provides you with a working environment and interface to the operating system. Usually there are several different shell programs installed. The shell program bash is one of the most common ones.

finger <user_name> # shows which shell you are using
chsh -l # gives list of shell programs available on your system (does not work on all UNIX variants)
<shell_name> # switches to different shell

STDIN, STDOUT, STDERR, Redirections, and Wildcards

See LINUX HOWTOs

By default, UNIX commands read from standard input (STDIN) and send their output to standard out (STDOUT).

You can redirect them by using the following commands:

<beginning-of-filename>* # * is wildcard to specify many files
ls > file # prints ls output into specified file
command < my_file # uses file after '<' as STDIN
command >> my_file # appends output of one command to file
command | tee my_file # writes STDOUT to file and prints it to screen
command > my_file; cat my_file # writes STDOUT to file and prints it to screen
command > /dev/null # turns off progress info of applications by redirecting
# their output to /dev/null
grep my_pattern my_file | wc # Pipes (|) output of 'grep' into 'wc'
grep my_pattern my_non_existing_file 2 > my_stderr # prints STDERR to file

Useful shell commands

cat <file1> <file2> > <cat.out> # concatenate files in output file 'cat.out'
paste <file1> <file2> > <paste.out> # merges lines of files and separates them by tabs (useful for tables)
cmp <file1> <file2> # tells you whether two files are identical
diff <fileA> <fileB> # finds differences between two files
head -<number> <file> # prints first lines of a file
tail -<number> <file> # prints last lines of a file
split -l <number> <file> # splits lines of file into many smaller ones
csplit -f out fasta_batch "%^>%" "/^>/" "{*}" # splits fasta batch file into many files
# at '>'
sort <file> # sorts single file, many files and can merge (-m)
# them, -b ignores leading white space, ...
sort -k 2,2 -k 3,3n input_file > output_file # sorts in table column 2 alphabetically and
# column 3 numerically, '-k' for column, '-n' for
# numeric
sort input_file | uniq > output_file # uniq command removes duplicates and creates file/table
# with unique lines/fields
join -1 1 -2 1 <table1> <table2> # joins two tables based on specified column numbers
# (-1 file1, 1: col1; -2: file2, col2). It assumes
# that join fields are sorted. If that is not the case,
# use the next command:
sort table1 > table1a; sort table2 > table2a; join -a 1 -t "`echo -e '\t'`" table1a table2a > table3 # '-a <table>' prints all lines of specified table!
# Default prints only all lines the two tables have in
# common. '-t "`echo -e '\t'`" ->' forces join to
# use tabs as field separator in its output. Default is
# space(s)!!!
cat my_table | cut -d , -f1-3 # cut command prints only specified sections of a table,
# -d specifies here comma as column separator (tab is
# default), -f specifies column numbers.
grep # see chapter 4
egrep # see chapter 4

A Visual Introduction to Screen

http://blogamundo.net/code/screen/

http://fosswire.com/post/2008/08/video-tutorial-getting-started-with-gnu-screen/

Starting a New Screen Session

screen # Start a new session
screen -S <some-name> # Start a new session and gives it a name

Commands to Control Screen

Ctrl-a d # Detach from the screen session

Ctrl-a c # Create a new window inside the screen session

Ctrl-a Space # Switch to the next window

Ctrl-a a # Switch to the window that you were previously on

Ctrl-a " # List all open windows. Double-quotes " are typed with the Shift key

Ctrl-d or type exit # Exit out of the current window. Exiting form the last window will end the screen session

Ctrl-a [ # Enters the scrolling mode. Use Page Up and Page Down keys to scroll through the window. Hit the Enter key twice to return to normal mode.

Attaching to Screen Sessions

From any computer, you can attach to a screen session after SSH-ing into a server.

screen -r # Attaches to an existing session, if there is only one
screen -r # Lists available sessions and their names, if there are more then one session running
screen -r <some-name> # Attaches to a specific session
screen -r <first-few-letters-of-name> # Type just the first few letters of the name
# and you will be attached to the session you need

Destroying Screen Sessions

1. Terminate all programs that are running in the screen session. The standard way to do that is:

Ctrl-c

2. Exit out of your shell.

exit

3. Repeat steps 1 and 2 until you see the message:

[screen is terminating]

There may be programs running in different windows of the same screen session. That's why you may need to terminate programs and exit shells multiple time.

Tabs and a Reasonably Large History Buffer

For a better experience with screen, run

cp ~/.screenrc ~/.screenrc.backup 2> /dev/null
echo 'startup_message off
defscrollback 10240
caption always "%{=b dy}{ %{= dm}%H %{=b dy}}%={ %?%{= dc}%-Lw%?%{+b dy}(%{-b r}%n:%t%{+b dy})%?(%u)%?%{-dc}%?%{= dc}%+Lw%? %{=b dy}}"
' > ~/.screenrc

More on Terminating Processes

Terminating a Running Process

Simple One-Liner Shell Scripts

Web page for script download.

Renames many files *.old to *.new. To test things first, replace 'do mv' with 'do echo mv'.

for i in *.input; do mv $i ${i/\.old/\.new}; done
for i in *\ *; do mv "$i" "${i// /_}"; done # Replaces spaces in files by underscores

Run an application in loops on many input files.

for i in *.input; do ./application $i; done

Run fastacmd from BLAST program in loops on many *.input files and create corresponding *.out files.

for i in *.input; do fastacmd -d /data/../database_name -i $i > $i.out; done

Run SAM's target99 on many input files.

for i in *.pep; do target99 -db /usr/../database_name -seed $i -out $i; done

Search in many files for a pattern and print occurrences together with file names.

for j in 0 1 2 3 4 5 6 7 8 9; do grep -iH <my_pattern> *$j.seq; done

Example of how to run an interactive application (tmpred) that asks for file name input/output.

for i in *.pep; do echo -e "$i\n\n17\n33\n\n\n" | ./tmpred $i > $i.out; done

Run BLAST2 for all *.fasa1/*.fasta2 file pairs in the order specified by file names and write results into one file.

for i in *.fasta1; do blast2 -p blastp -i $i -j ${i/_*fasta1/_*fasta2} >> my_out_file; done

This example uses two variables in a for loop. The content of the second variable gets specified in each loop by a replace function.

Runs BLAST2 in all-against-all mode and writes results into one file ('-F F' turns low-complexity filter off).

for i in *.fasta; do for j in *.fasta; do blast2 -p blastp -F F -i $i -j $j >> my_out_file; done; done;

How to write a real shell script

create file which contains in first line:

#!/bin/bash

place shell commands in file

run <chmod +x my_shell_script> to make it executable

run shell script like this: ./my_shell_script

when you place it into /usr/local/bin you only type its name from any user account

Simple One-Liner Perl Scripts

Small collection of useful one-liners:

perl -p -i -w -e 's/pattern1/pattern2/g' my_input_file
# Replaces a pattern in a file by a another pattern using regular expressions.
# $1 or \1: back-references to pattern placed in parentheses
# -p: lets perl know to write program
# -i.bak: creates backup file *.bak, only -i doesn't
# -w: turns on warnings
# -e: executable code follows

Parse lines based on patterns:

perl -ne 'print if (/my_pattern1/ ? ($c=1) : (--$c > 0)); print if (/my_pattern2/ ? ($d = 1) : (--$d > 0))' my_infile > my_outfile
# Parses lines that contain pattern1 and pattern2.
# The following lines after the pattern can be specified in '$c=1' and '$d=1'.
# For logical OR use this syntax: '/(pattern1|pattern2)/'.

Remote Copy: wget, scp, ncftp

wget: File Download from the Web

wget ftp://ftp.ncbi.nih.... # file download from www; add option '-r' to download entire directories

scp: Secure Copy Between Machines

General Syntax

scp source target # Use form 'userid@machine_name' if your local and remote user ids are different.
# If they are the same you can use only 'machine_name'.

Examples

scp user@remote_host:file.name . # Copies file from server to local machine (type from local
# machine prompt). The '.' copies to pwd, you can specify # here any directory, use wildcards to copy many files.

scp file.name user@remote_host:~/dir/newfile.name
# Copies file from local machine to server.

scp -r user@remote_host:directory/ ~/dir
# Copies entire directory from server to local machine.

Nice FTP

ncftp
ncftp> open ftp.ncbi.nih.gov
ncftp> cd /blast/executables
ncftp> get blast.linux.tar.Z (skip extension: @)
ncftp> bye

Archiving and Compressing

Creating Archives

tar -cvf my_file.tar mydir/ # Builds tar archive of files or directories. For directories, execute command in parent directory. Don't use absolute path.
tar -czvf my_file.tgz mydir/ # Builds tar archive with compression of files or directories. For
# directories, execute command in parent directory. Don't use absolute path.
zip -r mydir.zip mydir/ # Command to archive a directory (here mydir) with zip.
tar -jcvf mydir.tar.bz2 mydir/ # Creates *.tar.bz2 archive

Viewing Archives

tar -tvf my_file.tar
tar -tzvf my_file.tgz

Extracting Archives

tar -xvf my_file.tar
tar -xzvf my_file.tgz
gunzip my_file.tar.gz # or unzip my_file.zip, uncompress my_file.Z,
# or bunzip2 for file.tar.bz2
find -name '*.zip' | xargs -n 1 unzip # this command usually works for unzipping
# many files that were compressed under Windows
tar -jxvf mydir.tar.bz2 # Extracts *.tar.bz2 archive

Try also:

tar zxf blast.linux.tar.Z
tar xvzf file.tgz

Important options:

f: use archive file

p: preserve permissions

v: list files processed

x: exclude files listed in FILE

z: filter the archive through gzip

Simple Installs

Systems-wide installations

Installations for systems-wide usage are the responsibility of system administrator To find out if an application is installed, type:

which my_application
whereis my_application_name # searches for executables in set of directories,
# doesn't depend on your path

Most applications are installed in /usr/local/bin or /usr/bin

You need root permissions to write to these directories

Perl scripts go into /usr/local/bin, Perl modules (*.pm) into /usr/local/share/perl/5.8.8/

To copy executables in one batch, use command:

cp `find -perm -111 -type f` /usr/local/bin

Applications in user accounts

Create a new directory, download application into this directory, unpack it (see chapter 13) and follow package-specific installation instructions. Usually you can then already run this application when you specify its location e.g.: /home/user/my_app/blastall. If you want you can add this directory to your PATH by typing from this directory:

PATH=.:$PATH; export PATH # this allows you to run application by providing only its name; when you do echo $PATH you will see .: added to PATH.

Installation of RPMs

RPMs are installable software packages used in the following Linux distributions: RedHat, CentOS, Fedora, SuSe, and others.

rpm -i application_name.rpm

To check which version of RPM package is installed, type:

rpm --query <package_name>

Help and upgrade files for RPMs can be found at http://rpmfind.net/.

Installation of Debian Packages

Deb's are installable software packages used in the following Linux distributions: Debain, Ubuntu, and others.

Check whether your application is available at: http://packages.debian.org/stable/, then you type (no need to download):

apt-cache search phylip # searches for application "phylip" from command line
apt-cache show phylip # provides description of the package (see also: aptitude show)

aptitude install phylip # example for phylip install, manuals can be found in
# /usr/doc/phylip/, use zless or lynx to read documentation
# (don't unzip).

aptitude update # do once a month do update Debian packages
aptitude upgrade -u # to upgrade after update from above
dpkg -i # install data package from local package file (e.g. after
# download)

aptitude # Debian package managing interface (Ctrl-t opens menus)
aptitude search vim # search for packages on system and in Debian depositories
aptitude show vim # show detailed information about the package

Recommendation: Use "aptitude" everywhere instead of "apt-get". Arguments are the same in aptitude. By using it instead of "apt-get" you will have a log of all installations in /var/log/aptitude.

Recommendation: Use the aptitude GUI by running "aptitude" without arguments. You will need to learn some key strokes (keyboard combinations).

Devices

Mount/unmount: usb, floppy, cdrom, etc.

mount /media/usb
umount /media/usb
mount /media/cdrom
eject /media/cdrom
mount /media/floppy

Environment Variables

xhost user@host # adds X permissions for user on server.
echo $DISPLAY # shows current display settings
export DISPLAY=<local_IP>:0 # change environment variable
unsetenv DISPLAY # removes display variable
env # prints all environment variables

List of directories that the shell will search when you type a command:

echo $PATH

You can edit your default DISPLAY setting for your account by adding it to file .bash_profile

Exercises

Exercise 1 1. Download proteome of Halobacterium spec. with wget and look at it:

wget ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halobacterium_sp_uid217/AE004437.faa

less AE004437.faa # press q to quit

2. Simple Analysis:

a) How many predicted proteins are there?

grep '^>' AE004437.faa --count

b) How many proteins contain the pattern "WxHxxH" or "WxHxxHH"?

egrep 'W.H..H{1,2}' AE004437.faa --count

c) Use the find function (/) in 'less' to fish out the protein IDs containing the pattern or more elegantly do it with awk:

awk --posix -v RS='>' '/W.H..(H){1,2}/ { print ">" $0;}' AE004437.faa | less # press q to quit

3. Create a BLASTable database with formatdb:

ls # before

formatdb -i AE004437.faa -p T -o T

ls # after

'-p F' for nucleotide and '-p T' for protein database; '-o T' parse SeqId and create indexes

4. Generate myseq.fasta

a) Generate list of sequence IDs for the above pattern match result (i.e. retrieve my_IDs from step 2c). Alternatively, download the pre-generated file with wget.

b) Retrieve the corresponding sequences for these IDs with the fastacmd command from the blastable database:

wget http://biocluster.ucr.edu/~tgirke/Documents/UNIX/my_IDs

fastacmd -d AE004437.faa -i my_IDs > myseq.fasta

less myseq.fasta # press q to quit

5. (Optional) Looking at several different patterns:

a) Generate several lists of sequence IDs from various pattern match results (i.e. retrieve a.my_ids, b.my_ids, and c.my_ids from step 2c).

b) Retrieve the sequences in one step using the fastacmd in a for-loop:

for i in *.my_ids; do fastacmd -d AE004437.faa -i $i > $i.fasta; done

6. Run blastall with a few proteins in myseq.fasta against your newly created Halobacterium proteome database.
Create first a complete blast output file including alignments. In a second step use the 'm -8' option to obtain a tabular output (i.e. tab separated values).

blastall -p blastp -i myseq.fasta -d AE004437.faa -o blastp.out -e 1e-6 -v 10 -b 10
blastall -p blastp -i myseq.fasta -d AE004437.faa -m 8 -e 1e-6 > blastp.tab

less blastp.out # press q to quit
less -S blastp.tab # -S disables line wrapping, press q to quit

The filed descriptions of the Blast tabular output (from the "-m 8" option) are available here.
1 Query (The query sequence id)
2 Subject (The matching subject sequence id)
3 % id
4 alignment length
5 mismatches
6 gap openings
7 q.start
8 q.end
9 s.start
10 s.end
11 e-value
12 bit score

Is your blastp.out file equivalent to this one?

7. Parse blastall output into Excel spread sheet

a) Using biocore parser

blastParse -i blastp.out -o blast.xls -c 5

b) Using BioPerl parser

bioblastParse.pl blastp.out > blastparse.txt

Exercise 2

Split sample fasta batch file with csplit (use sequence file myseq.fasta from Exercise 1).

csplit -z myseq.fasta '/>/' '{*}'

Delete some of the files generated by csplit

Concatenate single fasta files from (step 1) into to one file with cat (e.g. "cat file1 file2 file3 > bigfile") .

BLAST two related sequences, retrieve the result in tabular format and use "comm" to identify common hit IDs in the two tables.

Exercise 3

Run HMMPFAM search with proteins from Exercise 1 against Pfam database (will take ~3 minutes)

hmmscan -E 0.1 --acc /srv/projects/db/pfam/2011-12-09-Pfam26.0/Pfam-A.hmm myseq.fasta > output.pfam

Easier to parse/process tabular output

hmmscan -E 0.1 --acc --tblout output.pfam /srv/projects/db/pfam/2011-12-09-Pfam26.0/Pfam-A.hmm myseq.fasta # also try --domtblout

Which query got the most hits? How many hits were found that query?

Exercise 4

Create multiple alignment with ClustalW (e.g. use sequences with 'W.H..HH' pattern)

clustalw myseq.fasta

mv myseq.aln myalign.aln

Exercise 5

Reformat alignment into PHYILIP format using 'seqret' from EMBOSS

seqret clustal::myalign.aln phylip::myalign.phylip

Exercise 6

Create neighbor-joining tree with PHYLIP

cp myalign.phylip infile
protdist # creates distance matrix (you may need to press 'R' and then 'Y')
cp outfile infile

neighbor # use default settings (press 'Y')
cp outtree intree

retree # displays tree and can use midpoint method for defining root of tree, my typical command sequence is: 'N' (until you see PHYLIP) 'Y' 'M' 'W' 'R' 'R' 'X'
cp outtree tree.dnd

Courtesy by : UC Reverside