Difference between revisions of "Troque Week 4"

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== Transcription and Translation “Taken to the Next Level” ==
 
== Transcription and Translation “Taken to the Next Level” ==
 
{{Template:Troque_LogIn}}
 
{{Template:Troque_LogIn}}
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Note: I collaborated with Lena Olufson when starting this assignment. We first decided to use <code>grep</code> in order to visually see where the pattern would be (it was actually my fault since we could've jumped to using <code>sed</code> right away, but I didn't read the assignment description thoroughly; I didn't notice that we were supposed to add the tags).
  
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In this assignment, we will be manipulating the file ''infA-E.coli-K12.txt''.
  
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=== Adding tags to the strand ===
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We start off by adding the -35 box of the promoter. The tag that we will add is
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...<minus35>...</minus>...
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We do this by using the <code>sed</code> command in order to "replace" the empty string around the pattern we are looking for. For this part, we are looking for the pattern <code>tt[gt]ac[at]</code>.
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Type the following command to insert the tags around the pattern on each line of its occurrence:
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sed "s/tt[gt]ac[at]/<minus35box> & </minus35box>\n/2" infA-E.coli-K12.txt
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Since we want to keep the pattern in the same file, but we want to add the tags around it, we use the ''&'' symbol.
  
 
{{Template:Troque_Journal}}
 
{{Template:Troque_Journal}}

Revision as of 03:41, 29 September 2015

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Transcription and Translation “Taken to the Next Level”

First, login to the LMU CS server using ssh. Type in the following in a command prompt (Windows) or terminal (Mac) window: 

ssh <username@my.cs.lmu.edu>

Enter your password. Note: You will not visibly see the cursor move when typing in your password so just keep typing. Then change directories to dondi's using the following commands to find the practice files and other miscellaneous files: 

cd ~dondi/xmlpipedb/data

Here, you can use the command ls in order to see the list of files in the directory. Then we can start manipulating some files. Note: I collaborated with Lena Olufson when starting this assignment. We first decided to use grep in order to visually see where the pattern would be (it was actually my fault since we could've jumped to using sed right away, but I didn't read the assignment description thoroughly; I didn't notice that we were supposed to add the tags).

In this assignment, we will be manipulating the file infA-E.coli-K12.txt.

Adding tags to the strand

We start off by adding the -35 box of the promoter. The tag that we will add is 

...<minus35>...</minus>...

We do this by using the sed command in order to "replace" the empty string around the pattern we are looking for. For this part, we are looking for the pattern tt[gt]ac[at].

Type the following command to insert the tags around the pattern on each line of its occurrence: 

sed "s/tt[gt]ac[at]/<minus35box> & </minus35box>\n/2" infA-E.coli-K12.txt

Since we want to keep the pattern in the same file, but we want to add the tags around it, we use the & symbol.

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