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Transcript

  • 1. Unix Text Editing, Printing, and File Transfers
  • 2. 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
  • 3. 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.
  • 4. 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
  • 5. 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”
  • 6. 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.
  • 7.  
  • 8. 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.
  • 9. 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 .
  • 10. 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-c
      • If 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
  • 11. 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
  • 12. 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.
  • 13. 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
  • 14. 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.
  • 15. 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 Editor
    • http://www.leeds.ac.uk/iss/documentation/beg/beg6.pdf
  • 16. 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
  • 17. 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.
  • 18. 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 pileup
    • fastx profilesearch compare
    • tfastx stringsearch mfold
    • blast findpatterns prime
    • ssearch coilscan wordsearch
  • 19. 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.
  • 20. 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.
  • 21.
    • 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.
  • 22. 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.
  • 23.  
  • 24. 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
  • 25.  
  • 26. Saving Mail Messages as Files
    • Hit the &quot; E &quot; key to &quot;Export&quot; 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 &quot; Q &quot;