Flask jsonify a list of objects

Give your EqltByGene an extra method that returns a dictionary:

class EqltByGene(object):
    #

    def serialize(self):
        return {
            'gene_id': self.gene_id, 
            'gene_symbol': self.gene_symbol,
            'p_value': self.p_value,
        }

then use a list comprehension to turn your list of objects into a list of serializable values:

jsonify(eqtls=[e.serialize() for e in my_list_of_eqtls])

The alternative would be to write a hook function for the json.dumps() function, but since your structure is rather simple, the list comprehension and custom method approach is simpler.

You can also be really adventurous and subclass flask.json.JSONEncoder; give it a default() method that turns your EqltByGene() instances into a serializable value:

from flask.json import JSONEncoder

class MyJSONEncoder(JSONEncoder):
    def default(self, obj):
        if isinstance(obj, EqltByGene):
            return {
                'gene_id': obj.gene_id, 
                'gene_symbol': obj.gene_symbol,
                'p_value': obj.p_value,
            }
        return super(MyJSONEncoder, self).default(obj)

and assign this to the app.json_encoder attribute:

app = Flask(__name__)
app.json_encoder = MyJSONEncoder

and just pass in your list directly to jsonify():

return jsonify(my_list_of_eqtls)

You could also look at the Marshmallow project for a more full-fledged and flexible project for serializing and de-serializing objects to Python primitives that easily fit JSON and other such formats; e.g.:

from marshmallow import Schema, fields

class EqltByGeneSchema(Schema):
    gene_id = fields.Integer()
    gene_symbol = fields.String()
    p_value = fields.Float()

and then use

jsonify(eqlts=EqltByGeneSchema().dump(my_list_of_eqtls, many=True)

to produce JSON output. The same schema can be used to validate incoming JSON data and (with the appropriate extra methods), used to produce EqltByGene instances again.