scout/adapter/mongo/variant.py
def gene_variants(self, query=None,
                   category='snv', variant_type=['clinical'],
                   nr_of_variants=50, skip=0):
        """Return all variants seen in a given gene.

        If skip not equal to 0 skip the first n variants.

        Arguments:
            query(dict): A dictionary with querys for the database, including
            variant_type: 'clinical', 'research'
            category(str): 'sv', 'str', 'snv' or 'cancer'
            nr_of_variants(int): if -1 return all variants
            skip(int): How many variants to skip
        """

        mongo_variant_query = self.build_variant_query(query=query,
                                   category=category, variant_type=variant_type)

        sorting = [('rank_score', pymongo.DESCENDING)]

        if nr_of_variants == -1:
            nr_of_variants = 0 # This will return all variants
        else:
            nr_of_variants = skip + nr_of_variants

        result = self.variant_collection.find(
            mongo_variant_query
            ).sort(sorting).skip(skip).limit(nr_of_variants)

        return result
def gene_variants(self, query=None,
                   category='snv', variant_type=['clinical'],
                   nr_of_variants=50, skip=0):
        mongo_variant_query = self.build_variant_query(query=query,
                                   category=category, variant_type=variant_type)

        sorting = [('rank_score', pymongo.DESCENDING)]

        if nr_of_variants == -1:
            nr_of_variants = 0 # This will return all variants
        else:
            nr_of_variants = skip + nr_of_variants

        result = self.variant_collection.find(
            mongo_variant_query
            ).sort(sorting).skip(skip).limit(nr_of_variants)

        return result
def gene_variants ( self , query = None , category = 'snv' , variant_type = [ 'clinical' ] , nr_of_variants = 50 , skip = 0 ) : mongo_variant_query = self . build_variant_query ( query = query , category = category , variant_type = variant_type ) sorting = [ ( 'rank_score' , pymongo . DESCENDING ) ] if nr_of_variants == - 1 : nr_of_variants = 0 # This will return all variants else : nr_of_variants = skip + nr_of_variants result = self . variant_collection . find ( mongo_variant_query ) . sort ( sorting ) . skip ( skip ) . limit ( nr_of_variants ) return result
Return all variants seen in a given gene.

        If skip not equal to 0 skip the first n variants.

        Arguments:
            query(dict): A dictionary with querys for the database, including
            variant_type: 'clinical', 'research'
            category(str): 'sv', 'str', 'snv' or 'cancer'
            nr_of_variants(int): if -1 return all variants
            skip(int): How many variants to skip
Return all variants seen in a given gene .