relations_graph.py

from __future__ import print_function, unicode_literals
import os
import csv
import pygraphviz as pgv


if __name__ == '__main__':
    path_this = os.path.dirname(os.path.abspath(__file__))
    relations_file = os.path.join(path_this, os.pardir, 'relations.csv')
    output_file = os.path.join(path_this, os.pardir, 'relations.pdf')
    rows = []

    graph = pgv.AGraph(name='relations', directed=True, rankdir='LR')
    hgnc_style = {'color': 'lightgray', 'style': 'filled',
                   'fontname': 'arial'}
    be_style = {'color': 'pink', 'style': 'filled',
                   'fontname': 'arial'}
    edge_style = {'fontname': 'arial'}

    with open(relations_file) as f:
        csvreader = csv.reader(f, delimiter=str(u','), lineterminator='\r\n',
                               quoting=csv.QUOTE_MINIMAL,
                               quotechar=str(u'"'))
        nodes = set([])
        isa_edges = set([])
        partof_edges = set([])
        for row in csvreader:
            ns1, id1, rel, ns2, id2 = row
            def node_label(ns, id):
                return '%s:%s' % (ns, id)
            for ns, id in ((ns1, id1), (ns2, id2)):
                if ns == 'HGNC':
                    graph.add_node(node_label(ns, id), **hgnc_style)
                elif ns == 'FPLX':
                    graph.add_node(node_label(ns, id), **be_style)
            edge = (node_label(ns1, id1), node_label(ns2, id2))
            if rel == 'isa':
                graph.add_edge(edge, label='isa', **edge_style)
            elif rel == 'partof':
                graph.add_edge(edge, label='partof', **edge_style)

    graph.draw(output_file, prog='dot')