mysql example fetch gene coordinates (snippet)

Python mysql example 'fetch gene coordinates'

Functions in program:

• def fetch_gene_coordinates(gene_name,build):

Modules used in program:

• import _mysql

python fetch gene coordinates

Python mysql example: fetch gene coordinates

# Note: Requires mysqldb; install using:
# pip install MySQL-python
from MySQLdb.constants import FIELD_TYPE
import _mysql

db = None

def fetch_gene_coordinates(gene_name,build):
    global db # db is global to prevent reconnecting.
    if db is None:
        print('connect')
        conv= { FIELD_TYPE.LONG: int }
        db = _mysql.connect(host='genome-mysql.cse.ucsc.edu',user='genome',passwd='',db=build,conv=conv)
    db.query("""SELECT * FROM kgXref INNER JOIN knownGene ON kgXref.kgID=knownGene.name WHERE kgXref.geneSymbol = '%s'""" % gene_name)

    r = db.use_result().fetch_row(how=1,maxrows=0)
    print(r)
    if len(r)>1:
        pass
    else:
        return r[0]['txStart'], r[0]['txEnd'], r[0]['chrom'],r[0]['strand']


print(fetch_gene_coordinates('klf1','mm9'))

Python links

• Learn Python: https://pythonbasics.org/
• Python Tutorial: https://pythonprogramminglanguage.com