Unix Text Editing, Printing, and File Transfers
Text Files <ul><li>Most bioinformatics work involves messing around with text files.  </li></ul><ul><li>DNA and protein se...
What is a Text Editor? <ul><li>A text editor is like a word processor on a personal computer, except that it does not appl...
Unix Text Editors <ul><li>There are many different text editors available for Unix computers. </li></ul><ul><ul><li>You ca...
Emacs <ul><li>The full name of the  Emacs  program is: &quot; GNU emacs, the Extensible, Customizable, Self-Documenting, R...
Starting emacs <ul><li>To start  Emacs , at the  >  command prompt, just type:  emacs   </li></ul><ul><li>To use  Emacs  t...
 
The Emacs Display <ul><li>The display in  Emacs  is divided into three basic areas.  </li></ul><ul><ul><ul><li>The top are...
Emacs Commands <ul><li>Emacs  uses  Control  and  Escape  characters to distinguish editor commands from text to be insert...
Save & Exit <ul><li>To save a file as you are working on it, type: </li></ul><ul><li>Control-x » Control-s </li></ul><ul><...
Moving Around <ul><li>The arrow keys on the keyboard work for moving around one line or one character at a time. </li></ul...
Type Text <ul><li>Once you move the cursor to the location in the file where you want to do some editing, you can just sta...
Cut, Copy, and Paste <ul><li>You can delete or move blocks of text. </li></ul><ul><ul><li>First move the cursor to the beg...
Getting Help in Emacs <ul><li>Emacs  has a built in help feature </li></ul><ul><ul><li>Just type:  Ctrl-h </li></ul></ul><...
Emacs Help on the Web <ul><li>Getting Started with Emacs </li></ul><ul><ul><li>http://www.cs.ucl.ac.uk/teaching/supportdoc...
Printing from Ranger <ul><li>The  Unix  print command on Ranger is  lpr -P  filename </li></ul><ul><ul><li>lpr  stands for...
GCG Figure Files <ul><li>Rather than directly printing graphical output from a  GCG  program, you should create a graphic ...
Using the Batch Queue <ul><li>GCG   has a feature known as the  Batch Queue  that allows large computing jobs to be comple...
FTP <ul><li>You will occasionally need to move files between your RCR account and a desktop computer  </li></ul><ul><ul><l...
FTP Login <ul><li>When you open an  FTP  program, you connect to  mcrcr0  just as you would with a  telnet  client. </li><...
<ul><li>You will automatically end up in your home directory. </li></ul><ul><li>Put  files from you PC to the server,  Get...
Access to e-mail <ul><li>Many people receive DNA sequences by e-mail.  </li></ul><ul><ul><li>It would be convenient to acc...
 
View Your Mail <ul><li>Make sure to set your usual e-mail program to “leave mail on server” </li></ul><ul><li>Your recent ...
 
Saving Mail Messages as Files <ul><li>Hit the &quot; E &quot; key to &quot;Export&quot; a message and save it as a file.  ...
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Unix Lec2

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Unix Lec2

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

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