Week 4 E-notes Eyanosch - Revision history

Eyanosch: made a few alterations to the code for question 1, realizing I had the wrong TSS after reading the directions again. I counted from the last nucleotide in the minus 10 box rather than the first

2015-09-29T01:57:27Z

made a few alterations to the code for question 1, realizing I had the wrong TSS after reading the directions again. I counted from the last nucleotide in the minus 10 box rather than the first

Eyanosch at 00:46, 29 September 2015

2015-09-29T00:46:05Z

Eyanosch: saving my code

2015-09-29T00:45:29Z

saving my code

Eyanosch at 00:16, 29 September 2015

2015-09-29T00:16:46Z

Eyanosch: added current code and changes

2015-09-29T00:16:05Z

added current code and changes

Eyanosch: thoughts while doing this weeks hw, having trouble recombining lines after breaking them into two

2015-09-29T00:12:12Z

thoughts while doing this weeks hw, having trouble recombining lines after breaking them into two

Eyanosch: added code and description of terminator sequence

2015-09-24T23:16:22Z

added code and description of terminator sequence

Eyanosch: notes for week 4 assigment

2015-09-24T23:13:09Z

notes for week 4 assigment

New page

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

← Older revision		Revision as of 01:57, 29 September 2015
Line 28:		Line 28:
	grep "aaaaggt.gcctttt" \| sed "s/aaaaggtc.tttttatt/ <terminator>&<\/terminator> /g" \|		grep "aaaaggt.gcctttt" \| sed "s/aaaaggtc.tttttatt/ <terminator>&<\/terminator> /g" \|
	sed "s/atg/ <start codon>&<\/start codon> /4" \| sed "s/tga/ <stop codon>&<\/stop codon> /11"		sed "s/atg/ <start codon>&<\/start codon> /4" \| sed "s/tga/ <stop codon>&<\/stop codon> /11"
		+
		+
		+	*After making a few adjustments:
		+	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/ <MINUS10BOX> & <\/MINUS10BOX> /" \| sed "s/cttgcc/&\n/g" \| sed "2s/g/ <TSS>&<\/TSS>/1" \| sed ':a;N;$!ba;s/\n//g' \|
		+	sed "s/gagg/ <RBS>&<\/RBS> /g" \| grep "aaaaggt.gcctttt" \| sed "s/aaaaggtc.tttttatt/ <TERMINATOR>&<\/TERMINATOR> /g" \|
		+	sed "s/tac/ <START CODON>&<\/START CODON> /7" \| sed "s/att/ <STOP CODON>&<\/STOP CODON> /11"

← Older revision		Revision as of 00:46, 29 September 2015
Line 23:		Line 23:

	Question 1 code:		Question 1 code:
−	eyanosch@ab201:/nfs/home/dondi/xmlpipedb/data$ 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> /" \| sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS>/1" \| sed ':a;N;$!ba;s/\n//g' \| sed "s/gagg/ <RBS>&<\/RBS> /g" \| grep "aaaaggt.gcctttt" \| sed "s/aaaaggtc.tttttatt/ <terminator>&<\/terminator> /g" \| sed "s/atg/ <start codon>&<\/start codon> /4" \| sed "s/tga/ <stop codon>&<\/stop codon> /11"	+	eyanosch@ab201:/nfs/home/dondi/xmlpipedb/data$ 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> /" \|
		+	sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS>/1" \| sed ':a;N;$!ba;s/\n//g' \| sed "s/gagg/ <RBS>&<\/RBS> /g" \|
		+	grep "aaaaggt.gcctttt" \| sed "s/aaaaggtc.tttttatt/ <terminator>&<\/terminator> /g" \|
		+	sed "s/atg/ <start codon>&<\/start codon> /4" \| sed "s/tga/ <stop codon>&<\/stop codon> /11"

← Older revision		Revision as of 00:45, 29 September 2015
Line 20:		Line 20:
	sed "s/cattat/ <minus 10box> & <\/minus10box> \" \| sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS> /1" \| sed ':a;N;$!bs;s/\n//g' \|		sed "s/cattat/ <minus 10box> & <\/minus10box> \" \| sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS> /1" \| sed ':a;N;$!bs;s/\n//g' \|
	sed "2s/gagg/ <RBS>&<\/RBS> /" \| grep "aaaaggt.*gcctttt"		sed "2s/gagg/ <RBS>&<\/RBS> /" \| grep "aaaaggt.*gcctttt"
		+
		+
		+	Question 1 code:
		+	eyanosch@ab201:/nfs/home/dondi/xmlpipedb/data$ 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> /" \| sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS>/1" \| sed ':a;N;$!ba;s/\n//g' \| sed "s/gagg/ <RBS>&<\/RBS> /g" \| grep "aaaaggt.gcctttt" \| sed "s/aaaaggtc.tttttatt/ <terminator>&<\/terminator> /g" \| sed "s/atg/ <start codon>&<\/start codon> /4" \| sed "s/tga/ <stop codon>&<\/stop codon> /11"

← Older revision		Revision as of 00:16, 29 September 2015
Line 17:		Line 17:

	Code as is:		Code as is:
−	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> \" \| sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS> /1" \| sed ':a;N;$!bs;s/\n//g' \| sed "2s/gagg/ <RBS>&<\/RBS> /" \| grep "aaaaggt.*gcctttt"	+	cat infA-E.coli-K12.txt \| grep "[ct]at[at]at" \| grep "tt[gt]ac[at]" \| sed "s/tttact/ <minus35box> & <\/minus35box> /g" \|
		+	sed "s/cattat/ <minus 10box> & <\/minus10box> \" \| sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS> /1" \| sed ':a;N;$!bs;s/\n//g' \|
		+	sed "2s/gagg/ <RBS>&<\/RBS> /" \| grep "aaaaggt.*gcctttt"

← Older revision		Revision as of 00:16, 29 September 2015
Line 15:		Line 15:

	* 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		* 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
		+
		+	Code as is:
		+	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> \" \| sed "s/ccggttc/&\n/g" \| sed "2s/a/ <TSS>&<\/TSS> /1" \| sed ':a;N;$!bs;s/\n//g' \| sed "2s/gagg/ <RBS>&<\/RBS> /" \| grep "aaaaggt.*gcctttt"

@@ Line 4: / Line 4: @@
 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"
+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
@@ Line 10: / Line 10: @@
 | sed "s/aaaaggt.*tttttatt/ <Terminator>&<\/Terminator/g"
 *adds the description of the terminator sequence

← Older revision		Revision as of 23:16, 24 September 2015
Line 7:		Line 7:

	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
		+
		+	\| sed "s/aaaaggt.*tttttatt/ <Terminator>&<\/Terminator/g"
		+	*adds the description of the terminator sequence