https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?action=history&feed=atom&title=Talk%3ABklein7_Week_4
Talk:Bklein7 Week 4 - Revision history
2026-06-08T06:04:31Z
Revision history for this page on the wiki
MediaWiki 1.25.1
https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Talk:Bklein7_Week_4&diff=1829&oldid=prev
Bklein7: added note to preliminary code section
2015-09-28T18:40:01Z
<p>added note to preliminary code section</p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 18:40, 28 September 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L13" >Line 13:</td>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>**sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>**sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>**sed "s/x/y/1$" - does not work</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>**sed "s/x/y/1$" - does not work</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**answer: use rev commands!</ins></div></td></tr>
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Bklein7
https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Talk:Bklein7_Week_4&diff=1677&oldid=prev
Bklein7: Copied over preliminary code and troubleshooting guidelines from after class work on the assignment
2015-09-25T00:30:28Z
<p>Copied over preliminary code and troubleshooting guidelines from after class work on the assignment</p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 00:30, 25 September 2015</td>
</tr><tr><td colspan="2" class="diff-lineno" id="L1" >Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">==Notes==</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*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].</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>*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].</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">==Preliminary Code==</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">  sed "s/tt[gt]ac[at]/<minus35box>&<\/minux35box>\n/1" infA-E.coli-K12.txt | sed -r "2s/^.    </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">  {17}/&<minus10box>/g" | sed "s/<minus10box>....../&<\/minus10box/g" | sed -r </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">  "s/<\/minus10box>.{11}/&<tss>/g" | sed "s/<tss>./&<\/tss/g" | sed "s/gagg/<rbs>&<\/rbs>\n/g" </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">  | sed "3s/atg/<start_codon>&<\/start_codon>\n/1" | sed "s/aaaaggt/\n<terminator>&/g" | sed -</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">  r "s/aaaaggt.*gcctttt.{4}/&<\/terminator>/g" | sed "4s/.../& /g" | sed -r </ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">  "4s/taa|tag|tga/<stop_codon>&<\/stop_codon>/g" | sed "4s/ //g" | sed ':a;N;$!ba;s/\n//g'</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">*String together redundant sed commands with ; or find a way to make them more compact</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">*Verify when the terminator sequence starts</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">*Is there a way to count backwards in a line with sed? or so replace only the last instance that matches? previous experiments</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**sed "s/x.*$/y/g" - does not work, wild card overtakes the last instance</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div><ins style="font-weight: bold; text-decoration: none;">**sed "s/x/y/1$" - does not work</ins></div></td></tr>
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Bklein7
https://xmlpipedb.lmucs.io/biodb/fall2015/index.php?title=Talk:Bklein7_Week_4&diff=1619&oldid=prev
Bklein7: Added link to slides presented in 9/22 lecture
2015-09-22T22:50:02Z
<p>Added link to slides presented in 9/22 lecture</p>
<p><b>New page</b></p><div>*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].</div>
Bklein7