Saturday, June 23, 2007

One-liner for mapping Agilent Microarray ID to Affymetrix Genechip ID

echo "
SELECT
mmusculus_gene_ensembl__xref_agilentprobe__dm.dbprimary_id,
mmusculus_gene_ensembl__xref_agilentprobe__dm.gene_stable_id,
mmusculus_gene_ensembl__xref_affy_mouse430_2__dm.dbprimary_id
FROM
mmusculus_gene_ensembl__xref_agilentprobe__dm,
mmusculus_gene_ensembl__xref_affy_mouse430_2__dm
WHERE
mmusculus_gene_ensembl__xref_agilentprobe__dm.dbprimary_id = 'A_52_P654624' AND
mmusculus_gene_ensembl__xref_agilentprobe__dm.gene_id_key = /
mmusculus_gene_ensembl__xref_affy_mouse430_2__dm.gene_id_key;" /
| mysql -h ensembldb.ensembl.org -A -uanonymous -D ensembl_mart_40

You need mysqlclient.

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