demo.py

import dash
import dash_html_components as html
import dash_core_components as dcc
import pandas as pd
from dash.dependencies import Input, Output
from itertools import cycle


class GeneSetDropdown:

    def __init__(self, gmt_file_name):
        self.gene_sets = pd.read_csv(gmt_file_name, sep="\t", header=None)
        self.set_names = self.gene_sets.iloc[:, 0].tolist()
        self.indices = self.gene_sets.index.tolist()

    def get_set(self, idx):
        return filter(lambda x: not pd.isnull(x), self.gene_sets.loc[idx].tolist()[2:])

    def make_component(self, id):
        return dcc.Dropdown(
            id=id,
            options=[{
                "label": label,
                "value": value
            } for label, value in zip(self.set_names, self.indices)]
        )


GSD = GeneSetDropdown("h.all.v6.1.symbols.gmt")
GSD_component = GSD.make_component('gene-set-dropdown')


class GeneSearchBox:

    def __init__(self, gmt_file_name):
        self.genes = set(pd.read_csv(
            gmt_file_name,
            sep="\t",
            header=None
        ).iloc[:, 2:].values.flatten().tolist())

    @staticmethod
    def make_component(id):
        return dcc.Textarea(
            id=id,
            value="",
            placeholder="Enter a whitespace-separated list of HUGO symbols",
        )

    def check_valid(self, hugo_id):
        return hugo_id in self.genes

    def get_gene_color(self, hugo_id):
        return 'green' if self.check_valid(hugo_id) else 'red'

    @staticmethod
    def parse_input(text_body):
        return text_body.split()

GSB = GeneSearchBox("h.all.v6.1.symbols.gmt")
GSB_component = GSB.make_component('gene-searchbox')

app = dash.Dash('Dash')

app.layout = html.Div([
    GSB_component,
    html.Div(id='gene-searchbox-parse'),
    GSD_component,
    html.Div(id='gene-set-list')
])


@app.callback(Output('gene-set-list', 'children'),
              [Input('gene-set-dropdown', 'value')])
def populate_gene_set_list(value):
    return [g + ' ' for g in GSD.get_set(value)]


@app.callback(Output('gene-searchbox-parse', 'children'),
              [Input('gene-searchbox', 'value')])
def populate_gene_search_results(value):
    attempted_genes = GSB.parse_input(value)
    return [html.Span(g + ' ', style={"color": GSB.get_gene_color(g)})
            for g in attempted_genes]


app.run_server(debug=True)