def _extract(vcf_id):
"""Extract the genotypes from a VCF and insert into the DB.
This also fills in a few fields in the vcfs table which aren't available
until the entire VCF has been read, e.g. the variant count.
Returns the vcf_id, or False if an error occurred.
"""
engine = sqlalchemy.create_engine(DATABASE_URI)
with tables(engine, 'vcfs') as (con, vcfs_table):
metadata = sqlalchemy.MetaData(bind=con)
metadata.reflect()
vcf = vcfs_table.select().where(vcfs_table.c.id == vcf_id).execute().fetchone()
# Validate the contents of the VCF before modifying the database.
reader, header_text, release = load_vcf(vcf['uri'])
# Fill in VCF header text, which is now available.
(vcfs_table.update()
.where(vcfs_table.c.id == vcf_id)
.values(vcf_header=header_text, vcf_release=release)
.execute())
insert_genotypes_with_copy(reader, engine,
default_values={'vcf_id': vcf_id},
temporary_dir=TEMPORARY_DIR)
update_extant_columns(metadata, con, vcf_id)
update_vcf_count(metadata, con, vcf_id)
return vcf_id
def _annotate(vcf_id):
if vcf_id == False:
return # An error must have occurred earlier.
engine = sqlalchemy.create_engine(DATABASE_URI)
# See if we have any guesses for a release version
with tables(engine, 'vcfs') as (con, vcfs):
vcf = vcfs.select().where(vcfs.c.id == vcf_id).execute().fetchone()
release = vcf['vcf_release']
if not release:
release = config.ENSEMBL_RELEASE
# Only runs the first time for this release.
EnsemblRelease(release).install()
with tables(engine, 'genotypes') as (con, genotypes):
metadata = sqlalchemy.MetaData(bind=con)
metadata.reflect()
annotations = get_varcode_annotations(genotypes, vcf_id, release)
tmp_table = Table('gene_annotations',
metadata,
Column('contig', Text, nullable=False),
Column('position', Integer, nullable=False),
Column('reference', Text, nullable=False),
Column('alternates', Text, nullable=False),
Column('gene_name', Text, nullable=True),
Column('transcript', Text, nullable=True),
Column('notation', Text, nullable=True),
Column('effect_type', Text, nullable=True),
prefixes=['TEMPORARY'])
try:
tmp_table.create()
write_to_table_via_csv(tmp_table, rows=annotations, connection=con)
# Add gene names from temp table to genotypes.
(genotypes.update()
.where(genotypes.c.contig == tmp_table.c.contig)
.where(genotypes.c.position == tmp_table.c.position)
.where(genotypes.c.reference == tmp_table.c.reference)
.where(genotypes.c.alternates == tmp_table.c.alternates)
.where(genotypes.c.vcf_id == vcf_id)
.values(
{
'annotations:gene_name': tmp_table.c.gene_name,
'annotations:transcript': tmp_table.c.transcript,
'annotations:effect_notation': tmp_table.c.notation,
'annotations:effect_type': tmp_table.c.effect_type
}
)).execute()
finally:
con.execute("DISCARD TEMP")
# We've added annotations:varcode_*, so update the columns to display.
update_extant_columns(metadata, con, vcf_id)
return vcf_id