Difference between revisions of "Stephen Louie Week 3"
From LMU BioDB 2013
(Added "XMLPipeDB Match Practice) |
(Edited numbering of "XMLPipeDB") |
||
| Line 22: | Line 22: | ||
#There are two unique matches. GO:0009165 appears 2 times. GO:0009168 appears 1 time. I believe GO:000916 is a specific strain of bacterium | #There are two unique matches. GO:0009165 appears 2 times. GO:0009168 appears 1 time. I believe GO:000916 is a specific strain of bacterium | ||
| − | |||
#There are two unique matches. "James K.D." appears 8238 times. "James A.A." appears once. \"James.*\ probably represents the name of an author. | #There are two unique matches. "James K.D." appears 8238 times. "James A.A." appears once. \"James.*\ probably represents the name of an author. | ||
| − | |||
#Match gave 165 occurrences. grep/wc gave 162 occurrences. Theses answers make sense due to the unique ways in which Match and grep/wc count for their occurrences. Match reads the entire file as a single line while grep/wc breaks and scans the file in chunks. The reasons grep/wc has less occurrences is because when the file is split up into chunks it can split a certain match in two pieces resulting in a lost match. Since Match looks at the file in a single line, none of the matches are at risk of being split apart. | #Match gave 165 occurrences. grep/wc gave 162 occurrences. Theses answers make sense due to the unique ways in which Match and grep/wc count for their occurrences. Match reads the entire file as a single line while grep/wc breaks and scans the file in chunks. The reasons grep/wc has less occurrences is because when the file is split up into chunks it can split a certain match in two pieces resulting in a lost match. Since Match looks at the file in a single line, none of the matches are at risk of being split apart. | ||
Revision as of 04:16, 13 September 2013
Contents |
Where's your stuff?
The icon changed from a note to a webpage
Complement of a Strand
The command I used to get the complement strand was:
cat prokaryote.txt | sed "y/atcg/tagc/"
Reading Frames
The six sets of text proccessing commands I used were:
cat prokaryote.txt | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed cat prokaryote.txt | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed cat prokaryote.txt | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed cat prokaryote.txt | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed cat prokaryote.txt | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed cat prokaryote.txt | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
XMLPipeDB Match Practice
- There are two unique matches. GO:0009165 appears 2 times. GO:0009168 appears 1 time. I believe GO:000916 is a specific strain of bacterium
- There are two unique matches. "James K.D." appears 8238 times. "James A.A." appears once. \"James.*\ probably represents the name of an author.
- Match gave 165 occurrences. grep/wc gave 162 occurrences. Theses answers make sense due to the unique ways in which Match and grep/wc count for their occurrences. Match reads the entire file as a single line while grep/wc breaks and scans the file in chunks. The reasons grep/wc has less occurrences is because when the file is split up into chunks it can split a certain match in two pieces resulting in a lost match. Since Match looks at the file in a single line, none of the matches are at risk of being split apart.
