Difference between revisions of "Jwoodlee Week 15"
From LMU BioDB 2015
(→Electronic Lab Notebook: added outline for individual reflection) |
(→Individual Reflection(Also on its own individual page here): added link to ind. refl.) |
||
| (19 intermediate revisions by the same user not shown) | |||
| Line 1: | Line 1: | ||
== Electronic Lab Notebook == | == Electronic Lab Notebook == | ||
| − | Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by | + | Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes: |
| + | This is what the final customized class looks like: | ||
| + | [[Image:FinalCustomizationsPart1.png]] | ||
| − | + | [[Image:FinalCustomizationsPart2.png]] | |
| − | + | A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines: | |
| − | + | ||
| − | + | [[Image: Gmbuilder.propertiesOriginal.png]] | |
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| − | + | ||
| + | This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on [[Jwoodlee Week 12 | Week 12]] and [[Jwoodlee Week 14 | Week 14]]. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below: | ||
| + | |||
| + | select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined; | ||
| + | |||
| + | == Individual Reflection(Found [[Jwoodlee Individual Reflection | here]]) == | ||
{{Template: Jwoodlee}} | {{Template: Jwoodlee}} | ||
Latest revision as of 18:26, 18 December 2015
Electronic Lab Notebook
Our GenMAPP users were reporting 416 missing genes from the .gdb which was a problem. Trixie found that 92 of these genes were in the XML file in such a way that led to the exporter missing them, the rest of the missing genes simply weren't in the XML file. Specifically, the genes were somewhere else in the file and weren't added to the OrderedLocusNames table by default. To capture these 92 elusive genes we consulted Dondi. Dondi edited the ShigellaflexneriUniProtSpeciesProfile class, which I had previously constructed, by adding a SQL query that captured the 92 missing genes:
This is what the final customized class looks like:
A further modification that was required was in the gmbuilder.properties file which we were supposed to edit to assist TallyEngine in its function, the initial customizations to this were the following lines:
This customization was insufficient in capturing the 92 missing genes. With the help of Dondi, Trixie and I replaced the insufficient SQL query with one that joined the missing 92 genes in the dbreference tag with the rest of the genes that were found by the default customization. Default customization can be found on Week 12 and Week 14. A sql union was used to execute this task which replaced the original sql query on gmbuilder.properties, as can be seen below:
select count(value) from (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?' union select extra as value from (select propertytype.value as extra from propertytype inner join dbreferencetype on propertytype.dbreferencetype_property_hjid = dbreferencetype.hjid where dbreferencetype.type = 'EnsemblBacteria' and dbreferencetype.id ~ 'AAN[0-9][0-9][0-9][0-9][0-9]' and propertytype.type = 'gene ID' and propertytype.value ~ 'SF[0-9][0-9][0-9][0-9]') as f left join (select value from genenametype where type = 'ordered locus' and value ~ '(CP|SF?)[0-9][0-9][0-9][0-9](\.[0-9])?') as g on f.extra = g.value where g.value is null) as combined;
Individual Reflection(Found here)
BIOL 367, Fall 2015, User Page, Team Page
| Weekly Assignments | Individual Journal Pages | Shared Journal Pages |
|---|---|---|
|
|
|
|
