unix lec2
TRANSCRIPT
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Unix Text Editing, Printing,
and File Transfers
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Text Files
• Most bioinformatics work involves messing around with text files.
• DNA and protein sequences, databases, results of similarity searches and multiple alignments are all stored on the computer as ordinary ASCII text files.
• To read, write, and edit these text files you must get familiar with a Text Editor program
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What is a Text Editor?
• A text editor is like a word processor on a personal computer, except that it does not apply formatting styles (bold, italics, different fonts etc.).
• Unix has line editors (view and edit one line at a time) and full screen editors.
• A screen editor loads an entire document into a buffer - allows you to jump to any point in the document.
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Unix Text Editors
• There are many different text editors available for Unix computers.– You can have multiple editors on one system
• vi - old, reliable, present on every Unix machine, completely and utterly user hostile
• jed - fairly simple, identical to eve on the old VMS system
• pico - extremely simple, perhaps too simple
• emacs - a good compromise between features and ease of use
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Emacs
• The full name of the Emacs program is: "GNU emacs, the Extensible, Customizable, Self-Documenting, Real-time Display Editor.”
• Emacs is free software produced by the Free Software Foundation (Boston, MA) and distributed under the GNU General Public License.– Open source software - Linux– GNU is an acronym for: “GNU is Not Unix”
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Starting emacs
• To start Emacs, at the > command prompt, just type: emacs
• To use Emacs to edit a file, type: emacs filename
(where filename is the name of your file)
• When Emacs is launched, it opens either a blank text window or a window containing the text of an existing file.
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The Emacs Display• The display in Emacs is divided into three
basic areas. • The top area is called the text window. The text
window takes up most of the screen, and is where the document being edited appears.
• Below the text window, there is a single mode line (in reverse type). The mode line gives information about the document, and about the Emacs session.
• The bottom line of the Emacs display is called the minibuffer. The minibuffer holds space for commands that you give to Emacs, and displays status information.
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Emacs Commands
• Emacs uses Control and Escape characters to distinguish editor commands from text to be inserted in the buffer.
Control-x means to hold down the control key, and type the letter x.
(You don't need to capitalize the x, or any other control character)
[ESCAPE] x means to press the escape key down, release it, and then type x.
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Save & Exit• To save a file as you are working on it, type:
Control-x » Control-s• To exit emacs and return to the Unix shell,
type: Control-x » Control-cIf you have made any changes to the file, Emacs will ask you if you want to save:
Save file /u/browns02/nrdc.msf? (y,n,!,.,q,C-r or C-h)
• Type “y” to save your changes and exit
• If you type “n”, then it will ask again:
Modified buffers exist; exit anyway? (yes or no)
• If you answer “no”, then it will return you to the file, you must answer “yes” to exit without saving changes
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Moving Around• The arrow keys on the keyboard work for
moving around one line or one character at a time.
• Some navigation commands:• Move to the Top of the file: [Esc] <
• Move to the End of the file: [Esc] >
• Next screen (page down): Ctrl-v
• Previous screen (page up): [Esc] v
• Start of the current line: Ctrl-a
• End of the current line: Ctrl-e
• Forward one word: [Esc] f
• Backward one word: [Esc] b
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Type Text
• Once you move the cursor to the location in the file where you want to do some editing, you can just start typing - just like in an ordinary word processor.
• The delete key should work to remove characters and inserted text will push existing text over.
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Cut, Copy, and Paste• You can delete or move blocks of text.
– First move the cursor to the beginning (or end) of the block of text.
– Then set a mark with: Ctrl-spacebar– Now move to the other end of the block of text
and Delete or Copy the block:• Delete: Ctrl-w• Copy: [Esc] w
– To Paste a copied block, move to the new location and insert with : Ctrl-y
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Getting Help in Emacs
• Emacs has a built in help feature– Just type: Ctrl-h– To get help with a specific command,
type: Ctrl-h k keys(where “keys” are the command keys that you type for
that command)
• Emacs has a built in tutorial: Ctrl-h t• this will be the primary exercise for this week’s
computer lab.
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Emacs Help on the Web• Getting Started with Emacs
http://www.cs.ucl.ac.uk/teaching/supportdocs/emacs.htm– by Johnathon Poole,University College London, Dept. of Computer
Science
• LinuxCentral: Emacs Beginner's HOWTO http://linuxcentral.com/linux/LDP/HOWTO/Emacs-Beginner-HOWTO.html
• The official GNU Emacs Manual http://www.gnu.org/manual/emacs/html_chapter/emacs_toc.html
• Getting Started With the Emacs Screen Editorhttp://www.leeds.ac.uk/iss/documentation/beg/beg6.pdf
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Printing from Ranger• The Unix print command on Ranger is lpr -P filename
– lpr stands for “line printer”
– The -P option specifies the name of the printer• There are lots of printers on the network; you need to tell the computer
where to send your print job
• The command printers will give you a list of the currently available printers.
• This works fine for any text file. Printing graphics is a bit more complicated.– Many GCG programs produce graphical output: MapPlot,
PlasmidMap, DrawTree, PepPlot, PlotStructure, etc.
– GCG can produce graphics in many different formats.
– Postscript generally works best on our system
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GCG Figure Files
• Rather than directly printing graphical output from a GCG program, you should create a graphic file in a format known as GCG Figure format - a .fig file.
• For any program that creates graphic output, use the -fig command option:
plotstructure -fig mygene.pep
• Then transform the .fig file into a Postscript file with the figure program.
• Finally, print the postscript file with the lpr -P command.• You can also transfer the .fig file to a Macintosh computer
by FTP and then use the Mac program GCGFigure to view and print the image.
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Using the Batch Queue• GCG has a feature known as the Batch Queue that allows
large computing jobs to be completed more efficiently.– you don't have to wait for a batch program to finish in order to
continue with your work– it allows the system to better balance the workload of multiple users
• To run a GCG program in batch mode, type the program name followed by the -bat modifier like this:
> fasta -bat• When your batch job is finished, the system will notify you• Here is a list of the programs that can be run in batch mode
fasta framesearch paupsearch
tfasta framealign pileupfastx profilesearch comparetfastx stringsearch mfoldblast findpatterns primessearch coilscan wordsearch
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FTP• You will occasionally need to move files
between your RCR account and a desktop computer – put sequences in, get output files and graphics off
• Use FTP (File Transfer Protocol) to do this.
• On the Macintosh, Fetch is the best FTP program.
• On Windows machines, WS_FTP works well.
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FTP Login• When you open an FTP program, you connect
to mcrcr0 just as you would with a telnet client.
• Your username and password are the same.
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• You will automatically end up in your home directory.
• Put files from you PC to the server, Get files from the server to your desktop machine.
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Access to e-mail
• Many people receive DNA sequences by e-mail. – It would be convenient to access those e-mail messages
directly from a telnet session on Ranger and save them as text files in your account.
• We have set up the pine program to do this– pine is set up to connect to the popmail server– If you have a popmail account, just type pine and
then your password to connect– If you use an e-mail server other than
popmail.med.nyu.edu, you will need to get in touch with us to modify your PINE settings.
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View Your Mail• Make sure to set your usual e-mail program
to “leave mail on server”
• Your recent mail messages will end up in your “Inbox”– connect to the mail server with pine and hit the
Return key a few times– Use the arrow keys to move to each message
and find the ones that you want to copy into your RCR account
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Saving Mail Messages as Files• Hit the "E" key to "Export" a message and
save it as a file.
• When you get the message:
EXPORT: Copy message to file in home directory:
you should type in a name for the new file, then hit Return. – Repeat this for each mail message that you want
to copy to your RCR account
• Quit Pine by typing "Q"