Class Notes

History

• Type history to view past commands
  • !#### will copy and execute commands
• Ctrl+R does most recent command

• chmod changes permission
  • e.g. "chmod 644 genetic-code.sed"

• Hitting tab twice will auto show all options to select from

Other Commands

• grep "ACTG" will look for typed letters ACTG in a string of text
  • if typed letters are present in a file, letters will appear red
    • grep "letters" file_name will search for letters in a file and open it
  • "." is a wildcard

"^" is the caret line, which only searches at the beginning of the line

• • "$" searches only at the end of the line
• "\"text.*\""
  • "*" matches any number of characters after text

• "wc" shows word count
  • Hit Ctrl D to finish typing text after wc command
    • first number tells # of lines
    • second number tells # of words
    • third number tells # of characters
  • combine commands with this notation: command | command
    • • you can string multiple commands together in one string

• "java -jar" opens java applications

• "&" repeats what you found (doesn't replace text, but adds to it)
  • E.g. sed "s/Ind.* /Wisconsin is still better than &/g"

Goals for Genetic Code

• break into 3s = s/.../ /g
• convert via genetic code = s/cgu/L/g; s/aug/M/g; (rest of genetic code letter assignments)
• drop 0-2 characters = s/^.//g
• reverse sequence = rev

s/aug/M/g

• Structure of command line
  • file > command | command > file

Assignment Notes

Week 3

1. Question

• java -jar xmlpipedb-match-1.1.1.jar "GO:000916." < 493.P_falciparum.xml

• Unique Matches = 2
• Appears twice in first line, once in second line

1. James yields 2 unique matches. First line james k.d. has 8238 matches, second line james a.a. has 1 match

• • "James" may refer to the person who sequenced all or a portion of falciparum.

1. Match ATG results in 1 unique match appearing 830101 times
   • grep and wc result in 502410 lines, 502410 words, and 35671048 characters
   • Answers make sense because Match is only looking for a specific instance when ATG appears, which would make its value lower than the grep | wc combo. grep | wc cannot differentiate specific pieces of text and yields any occurrence when the pattern ATG comes up.