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:

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]]

[[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 13 | Week 13]]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:

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;

  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;