def query(self):
if self.args.columns is not None:
# the user only wants to report a subset of the columns
query = "SELECT " + str(self.args.columns) + " FROM variants "
else:
# report the kitchen sink
query = "SELECT chrom, start, end, * %s " \
+ "FROM variants" % ", ".join(self.gt_cols)
query = sql_utils.ensure_columns(query, ['variant_id'])
# add any non-genotype column limits to the where clause
if self.args.filter:
query += " WHERE " + self.args.filter
# auto_rec and auto_dom candidates should be limited to
# variants affecting genes.
if self.model in ("auto_rec", "auto_dom", "comp_het") or \
(self.model == "de_novo" and self.args.min_kindreds is not None):
# we require the "gene" column for the auto_* tools
query = sql_utils.ensure_columns(query, ['gene'])
if self.args.filter:
query += " AND gene is not NULL ORDER BY chrom, gene"
else:
query += " WHERE gene is not NULL ORDER BY chrom, gene"
return query
def query(self):
if self.args.columns is not None:
# the user only wants to report a subset of the columns
query = "SELECT " + str(self.args.columns) + " FROM variants "
else:
# report the kitchen sink
query = "SELECT chrom, start, end, * %s " \
+ "FROM variants" % ", ".join(self.gt_cols)
query = sql_utils.ensure_columns(query, ['variant_id'])
# add any non-genotype column limits to the where clause
if self.args.filter:
query += " WHERE " + self.args.filter
# auto_rec and auto_dom candidates should be limited to
# variants affecting genes.
if self.model in ("auto_rec", "auto_dom", "comp_het") or \
(self.model == "de_novo" and self.args.min_kindreds is not None):
# we require the "gene" column for the auto_* tools
query = sql_utils.ensure_columns(query, ['gene'])
if self.args.filter:
query += " AND gene is not NULL ORDER BY chrom, gene"
else:
query += " WHERE gene is not NULL ORDER BY chrom, gene"
return query
def _construct_query(self):
"""
Construct the relevant query based on the user's requests.
"""
if self.args.columns is not None:
# the user only wants to report a subset of the columns
self.query = "SELECT " + str(self.args.columns) + \
" FROM variants "
else:
# report the kitchen sink
self.query = "SELECT *" + \
", gts, gt_types, gt_phases, gt_depths, \
gt_ref_depths, gt_alt_depths, gt_quals" + \
" FROM variants "
# add any non-genotype column limits to the where clause
if self.args.filter:
self.query += " WHERE " + self.args.filter
# auto_rec and auto_dom candidates should be limited to
# variants affecting genes.
if self.model == "auto_rec" or self.model == "auto_dom":
# we require the "gene" column for the auto_* tools
self.query = sql_utils.ensure_columns(self.query, ['gene'])
if self.args.filter:
self.query += " AND gene is not NULL ORDER BY gene"
else:
self.query += " WHERE gene is not NULL ORDER BY gene"
def _construct_query(self):
"""
Construct the relevant query based on the user's requests.
"""
if self.args.columns is not None:
# the user only wants to report a subset of the columns
self.query = "SELECT " + str(self.args.columns) + \
" FROM variants "
else:
# report the kitchen sink
self.query = "SELECT *" + \
", gts, gt_types, gt_phases, gt_depths, \
gt_ref_depths, gt_alt_depths, gt_quals" + \
" FROM variants "
# add any non-genotype column limits to the where clause
if self.args.filter:
self.query += " WHERE " + self.args.filter
# auto_rec and auto_dom candidates should be limited to
# variants affecting genes.
if self.model == "auto_rec" or self.model == "auto_dom":
# we require the "gene" column for the auto_* tools
self.query = sql_utils.ensure_columns(self.query, ['gene'])
if self.args.filter:
self.query += " AND gene is not NULL ORDER BY gene"
else:
self.query += " WHERE gene is not NULL ORDER BY gene"
def query(self):
if self.args.columns is not None:
# the user only wants to report a subset of the columns
query = "SELECT " + str(self.args.columns) + " FROM variants "
else:
# report the kitchen sink
query = "SELECT chrom, start, end, * %s " \
+ "FROM variants" % ", ".join(self.gt_cols)
query = sql_utils.ensure_columns(query, ['variant_id', 'gene'])
# add any non-genotype column limits to the where clause
if self.args.filter:
query += " WHERE " + self.args.filter
if hasattr(self.args, 'X'):
if self.args.X == []:
self.args.X = ['chrX', 'X']
part = "chrom IN (%s)" % ", ".join("'%s'" % x for x in self.args.X)
if " WHERE " in query:
query += " AND " + part
else:
query += " WHERE " + part
# auto_rec and auto_dom candidates should be limited to
# variants affecting genes.
if self.model in ("auto_rec", "auto_dom", "comp_het") or \
(self.model == "de_novo" and self.args.min_kindreds is not None):
# we require the "gene" column for the auto_* tools
if " WHERE " in query:
query += " AND gene is not NULL"
else:
query += " WHERE gene is not NULL"
# only need to order by gene for comp_het and when min_kindreds is used.
if self.model == "comp_het" or not (
self.args.min_kindreds in (None, 1)
and (self.args.families is None
or not "," in self.args.families)):
query += " ORDER by chrom, gene"
return query
def query(self):
if self.args.columns is not None:
# the user only wants to report a subset of the columns
query = "SELECT " + str(self.args.columns) + " FROM variants "
else:
# report the kitchen sink
query = "SELECT chrom, start, end, * %s " \
+ "FROM variants" % ", ".join(self.gt_cols)
query = sql_utils.ensure_columns(query, ['variant_id', 'gene'])
# add any non-genotype column limits to the where clause
if self.args.filter:
query += " WHERE " + self.args.filter
if hasattr(self.args, 'X'):
if self.args.X == []:
self.args.X = ['chrX', 'X']
part = "chrom IN (%s)" % ", ".join("'%s'" % x for x in self.args.X)
if " WHERE " in query:
query += " AND " + part
else:
query += " WHERE " + part
# auto_rec and auto_dom candidates should be limited to
# variants affecting genes.
if self.model in ("auto_rec", "auto_dom", "comp_het") or \
(self.model == "de_novo" and self.args.min_kindreds is not None):
# we require the "gene" column for the auto_* tools
if " WHERE " in query:
query += " AND gene is not NULL"
else:
query += " WHERE gene is not NULL"
# only need to order by gene for comp_het and when min_kindreds is used.
if self.model == "comp_het" or not (
self.args.min_kindreds in (None, 1) and
(self.args.families is None or not "," in self.args.families)):
query += " ORDER by chrom, gene"
return query
def format_query(self, query):
NEED_COLUMNS = [
"chrom", "rs_ids", "start", "gts", "type", "variant_id"
]
return ensure_columns(query, NEED_COLUMNS)
def format_query(self, query):
NEED_COLUMNS = ["chrom", "rs_ids", "start", "gts", "type", "variant_id"]
return ensure_columns(query, NEED_COLUMNS)