Ajvree Week 3

Week 3 Individual Assignment

Notes:

Shortcuts-

• cd to change directories, ls to view content
• up and down arrows to view command history, or type history, !number to redo that command
• CTRL R for reverse search- type in part of search, will recall past commands
• tab to fill in file name

• grep- text finder - looks for pattern: "ACTG" filename
• A followed by T with multiple things in between:
• . = "wildcard" "A......T"
• indicate beginning of line: ^ "^A......T"
• end of line: $ "A......T$"
• use previous command | wc to find word count for previously used file

• command|command
• wc- word count
• enter lines, then CTRL D
  1. lines, # words, #characters

To use xmldb match, enter java -jar xmlpipe.db-match-1.1.1.jar FIRST to give file, insert < sign in front
java -jar xmlpipedb-match-1.1.1.jar "A......T" < hs_ref_GRCh37_chr19.fa

1) "What Match command..."
-2 unique matches
-2,1
-what does info represent?

2) double quote w/in a double quote: "\"James.*\"" asterisk= zero or more
-unique 2
-2,1
-what info?

Reading Frames

Write 6 sets of text processing commands that, when given a nucleotide sequence, returns the resulting amino acid sequence, one for each possible reading frame for the nucleotide sequence. In other words, fill in the question marks:

XMLPipeDB Match Practice

For your convenience, the XMLPipeDB Match Utility (xmlpipedb-match-1.1.1.jar) has been installed in the ~dondi/xmlpipedb/data directory alongside the other practice files. Use this utility to answer the following questions:

   What Match command tallies the occurrences of the pattern GO:000916. in the 493.P_falciparum.xml file?
       How many unique matches are there?
       How many times does each unique match appear?
       What information do you think the pattern GO:000916. represents? 
   What Match command tallies the occurrences of the pattern \"James.*\" in the 493.P_falciparum.xml file?
       How many unique matches are there?
       How many times does each unique match appear?
       What information do you think the pattern \"James.*\" represents? 
   Use Match to count the occurrences of the pattern ATG in the hs_ref_GRCh37_chr19.fa file (this may take a while). Then, use grep and wc to do the same thing.
       What answer does Match give you?
       What answer does grep/wc give you?
       Do the answers make sense? Explain your response.

Ajvree (talk) 08:48, 12 September 2013 (PDT)
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