How do I get ensembl genome sizes with mysql?
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4.5 years ago
endrebak ▴ 930

To get genome sizes from UCSC I just use the following code:

import MySQLdb

def ucsc(genome, query):

    host = "genome-mysql.cse.ucsc.edu"
    user = "genome"
    db = genome

    conn = MySQLdb.Connection(host=host, user=user, db=db)

    df = pd.read_sql(query, conn)

    conn.close()

    return df


def chromosome_lengths(genome):

    query = 'select chrom,size from chromInfo'

    df = ucsc(genome, query)

    return pd.Series(df.size, index=df.chrom).to_dict()

But how do I get genome sizes from ensembl through mysql? For example for GRCz11 and GRCm38.p6.

Just giving me the mysql command line command is enough :)

ensembl • 1.2k views
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4.5 years ago
Emily 23k

The data is stored in the genome statistics table.

/usr/local/mysql/bin/mysql -h ensembldb.ensembl.org -u anonymous -P 5306
use danio_rerio_core_95_11;
select * from genome_statistics where statistic = "ref_length";
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Do you also know how to get chromosome sizes? :)

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