Fetch Ensembl gene IDs based on external ID.

ensembl_id.sh

#!/bin/sh

mysqluser='anonymous';
mysqlpass='';
mysqlhost='mysql.ebi.ac.uk';
mysqlport=4157;

function usage () {
    [ -n "$1" ] && echo $1
    cat <<USAGE
Fetches the EnsEMBL gene IDs associated with the specified external object ID.

Usage: $0 [-hHupP] database-name object-id

[options]
    -u user     : The MySQL user
    -p password : The MySQL password
    -h host     : The MySQL host
    -P port     : The MySQL TCP port
    -H          : This help message
USAGE
    exit 1
}

while getopts "Hu:p:h:P:" opt; do
     case $opt in 
        u) mysqluser="$OPTARG" ;;
        p) mysqlpass="$OPTARG" ;;
        h) mysqlhost="$OPTARG" ;;
        P) mysqlport="$OPTARG" ;;
        H) usage ;;
        ?) echo invalid or missing argument, type $0 -H for help; exit 1 ;;
    esac
done
shift $((OPTIND-1))

db_name=$1
object_id=$2
if [ -z "$db_name" -o -z "$object_id" ]; then
    usage "Missing required argument"
fi

mysql -t -h$mysqlhost -P$mysqlport -u$mysqluser --password=$mysqlpass $db_name <<SQL;
select external_db.db_name as source,
       gene_stable_id.stable_id as ensembl_id
  from gene
       left join gene_stable_id using (gene_id)
       left join transcript using (gene_id)
       left join transcript_stable_id using (transcript_id)
       left join translation using (transcript_id)
            join object_xref on (
                (ensembl_id = transcript_id and ensembl_object_type = 'Transcript') or
                (ensembl_id = translation_id and ensembl_object_type = 'Translation')
            )
       left join xref using (xref_id)
       left join external_db using (external_db_id)
 where xref.display_label like '$object_id'
 group by 1,2;
SQL

By default this script connects to the public EnsEMBL genomes database. An example usage is:

ensembl_id.sh arabidopsis_thaliana_core_12_65_10 APRR9_ARATH

Run with the -H option to get the options (mostly related to MySQL connections).