def testmusChid():
"""(Somewhat internal test) Check chromosome coord system id."""
import sys
sys.stdout.write("Mus Chromosome Coord System")
mus = ensembl.database('mus_musculus_core_56_37i')
coordsys = mus.chromosome_coord_system_id()
sys.stdout.write(" %d\n" % coordsys)
assert 1 == coordsys
def testBRCA2trans():
"""BRCA2 Transcripts."""
print "BRCA2 Transcripts"""
h**o = ensembl.database('homo_sapiens_core_62_37g')
# Sadly, the code now doesn't work with older releases
h**o = ensembl.Binomial('h**o sapiens')
ts = h**o.fetch_gene_name('BRCA2').Transcripts()
assert 6 == len(ts)
return ts
def testHseq():
"""Check (old) pymysql bug is not present.
(was originally detected by chromosome 20).
"""
dbid = 18559
print "H**o assembly 37a seq_region_id %d" % dbid
# Note: We require a particular release and assembly.
h**o = ensembl.database('homo_sapiens_core_56_37a')
cursor=h**o.conn.cursor()
cursor.execute('''select sequence from dna where
seq_region_id = %s;''', dbid)
result, = list(cursor)
result, = result
assert 37972 == len(result)