Exemple #1
0
    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
Exemple #2
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    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"
Exemple #5
0
    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
Exemple #6
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    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
Exemple #7
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 def format_query(self, query):
     NEED_COLUMNS = [
         "chrom", "rs_ids", "start", "gts", "type", "variant_id"
     ]
     return ensure_columns(query, NEED_COLUMNS)
Exemple #8
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 def format_query(self, query):
     NEED_COLUMNS = ["chrom", "rs_ids", "start", "gts", "type", "variant_id"]
     return ensure_columns(query, NEED_COLUMNS)