Difference between revisions of "Week 4 E-notes Eyanosch"
(added code and description of terminator sequence) |
(thoughts while doing this weeks hw, having trouble recombining lines after breaking them into two) |
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| Line 4: | Line 4: | ||
so far for the first question | so far for the first question | ||
| − | cat infA-E.coli-K12.txt | + | cat infA-E.coli-K12.txt | grep "[ct]at[at]at" | grep "tt[gt]ac[at]" | sed "s/tttact/ <minus35box> & <\/minus35box> /g" | sed "s/cattat/ <minus 10box> & <\/minus10box> \n/" | sed "s/a/ <TSS>&<\/TSS>/" | sed "2s/gagg/ <RBS>&<\/RBS> /" | grep "aaaaggt.*gcctttt" |
*the only problem that I'm having is only the second line shows when I add the grep "aaaaggt.*gcctttt" at the end to find the hairpin loop | *the only problem that I'm having is only the second line shows when I add the grep "aaaaggt.*gcctttt" at the end to find the hairpin loop | ||
| Line 10: | Line 10: | ||
| sed "s/aaaaggt.*tttttatt/ <Terminator>&<\/Terminator/g" | | sed "s/aaaaggt.*tttttatt/ <Terminator>&<\/Terminator/g" | ||
*adds the description of the terminator sequence | *adds the description of the terminator sequence | ||
| + | |||
| + | What I'm trying to do is use the sed ':a;N;$!ba;s/\n//g' format to combine line 1 with line 2 but I'm unable to do so. I think it has to do with the way I'm writing the code into the mac terminal. | ||
| + | My thinking process was that when finding the "a" for TSS I started a new line and counted down 12 nucleotides which happened to be an a, no prior nucletides were adenine. The problem is combining line 1 and 2 after finding the TSS. | ||
| + | |||
| + | * changed my plan of attack after going through more of the wiki. copied and asted the 3 sed commands for manipulating lines and it worked out | ||
Revision as of 00:12, 29 September 2015
3 command sequences
- one for each question
so far for the first question
cat infA-E.coli-K12.txt | grep "[ct]at[at]at" | grep "tt[gt]ac[at]" | sed "s/tttact/ <minus35box> & <\/minus35box> /g" | sed "s/cattat/ <minus 10box> & <\/minus10box> \n/" | sed "s/a/ <TSS>&<\/TSS>/" | sed "2s/gagg/ <RBS>&<\/RBS> /" | grep "aaaaggt.*gcctttt"
- the only problem that I'm having is only the second line shows when I add the grep "aaaaggt.*gcctttt" at the end to find the hairpin loop
| sed "s/aaaaggt.*tttttatt/ <Terminator>&<\/Terminator/g"
- adds the description of the terminator sequence
What I'm trying to do is use the sed ':a;N;$!ba;s/\n//g' format to combine line 1 with line 2 but I'm unable to do so. I think it has to do with the way I'm writing the code into the mac terminal. My thinking process was that when finding the "a" for TSS I started a new line and counted down 12 nucleotides which happened to be an a, no prior nucletides were adenine. The problem is combining line 1 and 2 after finding the TSS.
- changed my plan of attack after going through more of the wiki. copied and asted the 3 sed commands for manipulating lines and it worked out
