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Documented the :required_attributes option.

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commit 2de7464ac9cdb894ac4dca9fbd49d87ea907123e 1 parent 606efaf
Daz Oakley authored
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  1. +30 −0 README.rdoc
30 README.rdoc
@@ -130,6 +130,36 @@ possible to federate across more than two datasets in biomart itself.
Count queries are only allowed on single datasets.
+== Required Attributes
+As biomarts are generally big de-normalised data stores, a common task
+after receiving a set of results is to filter out rows that don't have
+information for a given attribute or set of attributes. A facility for
+doing this has been built into the gem.
+ htgt = "" )
+ res = htgt.datasets["mmusculus_gene_ensembl"].search(
+ :filters => {
+ "chromosome_name" => "1",
+ "start" => "1",
+ "end" => "10000000"
+ },
+ :attributes => [
+ "ensembl_gene_id", "ensembl_transcript_id",
+ "mouse_paralog_ensembl_gene", "mouse_paralog_chromosome"
+ ],
+ :required_attributes => ["mouse_paralog_ensembl_gene"]
+ )
+The above will perform a basic search and then automatically remove
+any result row that does not have a value for the "mouse_paralog_ensembl_gene"
+Note: You can specify more than one required attribute. If more than one
+required attribute is specified, ALL of these attributes must be present
+for a data row to be returned (it is using AND logic).
== Using a Proxy
If you need to channel all of your requests via a proxy, specify your
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