Talk:Bklein7 Week 3

• Accessing the cs lmu system:

my.cs.lmu.edu - in putty.exe
ssh username@my.cs.lmu.edu - in terminal

Commands

• • Exit
  • pwd : "print working directory" - shows the path to your current directory
  • ls : "list files"
    • blue- folders, white- documents
  • cd <name>: "change directory"
    • <name> = .. allows you to go up one directory
  • cat <filename> : shows contents of a file
  • more <filename> : shows truncated file contents that allows you to page around
    • space- page down
    • b- page up
    • q- quit truncated view
  • wc <filename> : word count of a file
    • display: lines / words / characters
  • grep "searchterm" <filename> : search for text
    • exclusively searchterm - " searchterm "
    • searchterm at end of line - "searchterm$"
    • searchterm at beginning of line - "^searchterm"
  • sed : replacing text
    • "s/<searchtext>/<replacetext>/g" <filename> : one time search and replace (words)
    • "y/<unqiuecharacters>/<newuniquecharacters>/" : letter by letter replacement
    • sed "s/.../& /g" <filename> to group sequence into codons
      • "..." any character
      • "&" what you just found
  • Aside: creating a new text file
    • echo 'text' >filename.txt

Putting Commands Together

• vertical bar ( | ) used to link commands together
  • ex. grep "King" movie_titles.txt | sed s/King/Queen/g
    • not necessary to reiterate file name, as you want the first command to act ONLY on the text of the second
• pipping commands without specifying a file name
  • the program will expect you to type in the input
  • Enter will initiate a new line
  • Command-D will end the input and begin pipping
• Echo "<sampletext>" will repeat the sampletext as an output
  • This is useful in pipping when you want to repeatedly analyze the same custom text

• Ways to access dondi's data folder
  1. cd /nfs/home/dondi/xmlpipedb/data
  2. cd ~dondi/xmlpipedb/data

Using XMLPipeDB Match

• Invoke with the command java -jar xmlpipedb-match-1.1.1.jar "<regex>"
  • This is the basic command and will prompt a text input
  • The regex is the search term that XMLPipeDB, like grep, will find
    • Unlike grep, this program offers extra statistics (total # unique matches and a count breakdown without echo'ing lines)
    • The regex can be broadened to find various search terms
      • ex. "d.g" would identify any three character sequences beginning with d and ending with g
      • ex. "do[gbd]" identifies a more restrictd three character sequence