Difference between revisions of "Stephen Louie Week 3"
From LMU BioDB 2013
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(Added corrections to #3 of XMLPipeDB practice) |
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==Complement of a Strand== | ==Complement of a Strand== | ||
| − | The command I used to get the complement strand was | + | 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 | ||
| + | |||
| + | '''Corrections: | ||
| + | |||
| + | '''cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed''' | ||
| + | |||
| + | '''cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed''' | ||
| + | |||
| + | '''cat prokaryote.txt | sed "y/atcg/tagc/" | 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. '''Match found 830,101 occurrences. grep/wc gave 502,410 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.''' | ||
| + | |||
| + | [[User:Slouie|Slouie]] ([[User talk:Slouie|talk]]) 11:18, 17 September 2013 (PDT) | ||
| + | [[Category:Journal Entry]] | ||
Latest revision as of 04:50, 20 September 2013
Contents |
[edit] Where's your stuff?
The icon changed from a note to a webpage
[edit] Complement of a Strand
The command I used to get the complement strand was:
cat prokaryote.txt | sed "y/atcg/tagc/"
[edit] 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
Corrections:
cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^.//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
cat prokaryote.txt | sed "y/atcg/tagc/" | rev | sed "s/^..//g" | sed "s/.../& /g" | sed "s/t/u/g" | sed -f genetic-code.sed
[edit] 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. Match found 830,101 occurrences. grep/wc gave 502,410 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.
