Difference between revisions of "Talk:Bklein7 Week 4"
From LMU BioDB 2015
(Added link to slides presented in 9/22 lecture) |
(Copied over preliminary code and troubleshooting guidelines from after class work on the assignment) |
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| + | ==Notes== | ||
*9/22- Slides from lecture can be found [https://mylmuconnect.lmu.edu/bbcswebdav/pid-1146580-dt-content-rid-1944592_1/courses/M_46692.201530/20150922_HGP_IntroBiolDB.pdf here]. | *9/22- Slides from lecture can be found [https://mylmuconnect.lmu.edu/bbcswebdav/pid-1146580-dt-content-rid-1944592_1/courses/M_46692.201530/20150922_HGP_IntroBiolDB.pdf here]. | ||
| + | ==Preliminary Code== | ||
| + | sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^. | ||
| + | {17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box/g" | sed -r | ||
| + | "s/<\/minus10box>.{11}/&<tss>/g" | sed "s/<tss>./&<\/tss/g" | sed "s/gagg/<rbs>&<\/rbs>\n/g" | ||
| + | | sed "3s/atg/<start_codon>&<\/start_codon>\n/1" | sed "s/aaaaggt/\n<terminator>&/g" | sed - | ||
| + | r "s/aaaaggt.*gcctttt.{4}/&<\/terminator>/g" | sed "4s/.../& /g" | sed -r | ||
| + | "4s/taa|tag|tga/<stop_codon>&<\/stop_codon>/g" | sed "4s/ //g" | sed ':a;N;$!ba;s/\n//g' | ||
| + | *String together redundant sed commands with ; or find a way to make them more compact | ||
| + | *Verify when the terminator sequence starts | ||
| + | *Is there a way to count backwards in a line with sed? or so replace only the last instance that matches? previous experiments | ||
| + | **sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance | ||
| + | **sed "s/x/y/1$" - does not work | ||
Revision as of 00:30, 25 September 2015
Notes
- 9/22- Slides from lecture can be found here.
Preliminary Code
sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.
{17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box/g" | sed -r
"s/<\/minus10box>.{11}/&<tss>/g" | sed "s/<tss>./&<\/tss/g" | sed "s/gagg/<rbs>&<\/rbs>\n/g"
| sed "3s/atg/<start_codon>&<\/start_codon>\n/1" | sed "s/aaaaggt/\n<terminator>&/g" | sed -
r "s/aaaaggt.*gcctttt.{4}/&<\/terminator>/g" | sed "4s/.../& /g" | sed -r
"4s/taa|tag|tga/<stop_codon>&<\/stop_codon>/g" | sed "4s/ //g" | sed ':a;N;$!ba;s/\n//g'
- String together redundant sed commands with ; or find a way to make them more compact
- Verify when the terminator sequence starts
- Is there a way to count backwards in a line with sed? or so replace only the last instance that matches? previous experiments
- sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance
- sed "s/x/y/1$" - does not work
