Exemple #1
0
def test():
    init()
    util._mkdir("../svg")
    html_file = open("../svg/templates.html", "w")
    for template in get_all_templates():
        template_svg = chemconvert.hash2svg(template, svg_size, svg_size, white, grey)
        html_file.write("<p>")
        template_svg.embed_in_html(html_file, "../svg/", template)
        html_file.write(template + "</p>")
        html_file.flush()
    html_file.close()
Exemple #2
0
def test():
    init()
    util._mkdir("../svg")
    html_file = open("../svg/templates.html", "w")
    for template in get_all_templates():
        template_svg = chemconvert.hash2svg(template, svg_size, svg_size,
                                            white, grey)
        html_file.write("<p>")
        template_svg.embed_in_html(html_file, "../svg/", template)
        html_file.write(template + "</p>")
        html_file.flush()
    html_file.close()
Exemple #3
0
def main():
    init()
    subdir = "motifs"
    motif_fullpath = html_path + "/motifs"
    util._mkdir(motif_fullpath)
    main_html_file = open(html_path + "/motifs.html", "w")
    
    anti_motif_list = []
    
    for size in motif_sizes:
        motifs = verify_file(size)
        motifs_t = motifs_templates(motifs)
        
        motif_hist = normalize_motifs(motifs)
        motif_hist_t = normalize_motifs(motifs_t)
    
        print "Generating all graphs of size %d ..." % size,
        all_graphs = generate_all_graphs(motif_hist, size)
        print "[DONE]"
        
        results = {}
        for h in all_graphs:
            G = chemconvert.hash2graph(h)
            template = G.template()
            count = int(motifs.get(h, 0))
            likelihoods = [0, 0]
            for i in range(2, size+1):
                likelihoods.append(get_likelihood(G, motif_hist, i))
            delta_l = likelihoods[-2] - likelihoods[-1]
            
            if (not results.has_key(template)):
                results[template] = []
            results[template].append((delta_l, likelihoods, count, h))

        main_html_file.write("<p>")
        size_html_file = util.embed_link(main_html_file, html_path, subdir + "/motifs%s" % size, "Motifs of size %s" % size)
        main_html_file.write("</p>")

        for (template, graph_list) in results.iteritems():
            size_html_file.write("<p>")
            template_svg = chemconvert.hash2svg(template, 200, 200, node_color=black, bond_color=grey)
            template_svg.embed_in_html(size_html_file, motif_fullpath, template)
            count_t = len(graph_list)
            if (count_t > 0):
                template_html_file = util.embed_link(size_html_file, motif_fullpath, template, "View all %d instances" % count_t)
                for (delta_l, likelihoods, count, h) in sorted(graph_list):
                    if (likelihoods[-1] <= log_zero and likelihoods[-2] <= log_zero):
                        continue
                    elif (likelihoods[-1] <= log_zero):
                        bond_color = red
                        anti_motif_list.append(h)
                    else:
                        #bond_color = (0, 255 * math.exp(-delta_l), 255 * (1 - math.exp(-delta_l)))
                        bond_color = green
                    
                    motif_svg = chemconvert.hash2svg(h, 150, 150, black, bond_color)
                    motif_svg.set_attribute("height", 200)
                    if (True): # add
                        #motif_svg.add(svg.Text((35, 25), h, 12, green))
                        l_string = ",".join(["%.1f" % l for l in likelihoods[2:]])
                        motif_svg.add(svg.Text((10, 160), "&#916;L = %.1f" % delta_l, font_size=12))
                        motif_svg.add(svg.Text((10, 175), l_string, font_size=12))
                        if (count > 0):
                            #motif_svg.add(svg.Text((35, 75), "diff = %.1f" % (l1-l0), 12, black))
                            motif_svg.add(svg.Text((10, 190), "count = %d" % count, font_size=12))
                        motif_svg.embed_in_html(template_html_file, motif_fullpath, h)
                    else: 
                        template_html_file.write("<p>")
                        motif_svg.embed_in_html(template_html_file, motif_fullpath, h)
                        template_html_file.write("<a href=\"" + h + ".svg\">" + h + "</a>")
                        template_html_file.write(", count = %d" % count)
                        for i in range(2, size+1):
                            template_html_file.write(", L(%d) = %.1f" % (i, likelihoods[i]))
                        template_html_file.write("</p>")
                template_html_file.close()
            else:
                size_html_file.write("No instances")
            
            size_html_file.write("</p>")
        size_html_file.close()
    main_html_file.close()
    
    util.write_text_file(anti_motif_list, "../results/stat/anti_motifs.txt")
    return
Exemple #4
0
def main():
    init()
    subdir = "motifs"
    motif_fullpath = html_path + "/motifs"
    util._mkdir(motif_fullpath)
    main_html_file = open(html_path + "/motifs.html", "w")

    anti_motif_list = []

    for size in motif_sizes:
        motifs = verify_file(size)
        motifs_t = motifs_templates(motifs)

        motif_hist = normalize_motifs(motifs)
        motif_hist_t = normalize_motifs(motifs_t)

        print "Generating all graphs of size %d ..." % size,
        all_graphs = generate_all_graphs(motif_hist, size)
        print "[DONE]"

        results = {}
        for h in all_graphs:
            G = chemconvert.hash2graph(h)
            template = G.template()
            count = int(motifs.get(h, 0))
            likelihoods = [0, 0]
            for i in range(2, size + 1):
                likelihoods.append(get_likelihood(G, motif_hist, i))
            delta_l = likelihoods[-2] - likelihoods[-1]

            if (not results.has_key(template)):
                results[template] = []
            results[template].append((delta_l, likelihoods, count, h))

        main_html_file.write("<p>")
        size_html_file = util.embed_link(main_html_file, html_path,
                                         subdir + "/motifs%s" % size,
                                         "Motifs of size %s" % size)
        main_html_file.write("</p>")

        for (template, graph_list) in results.iteritems():
            size_html_file.write("<p>")
            template_svg = chemconvert.hash2svg(template,
                                                200,
                                                200,
                                                node_color=black,
                                                bond_color=grey)
            template_svg.embed_in_html(size_html_file, motif_fullpath,
                                       template)
            count_t = len(graph_list)
            if (count_t > 0):
                template_html_file = util.embed_link(
                    size_html_file, motif_fullpath, template,
                    "View all %d instances" % count_t)
                for (delta_l, likelihoods, count, h) in sorted(graph_list):
                    if (likelihoods[-1] <= log_zero
                            and likelihoods[-2] <= log_zero):
                        continue
                    elif (likelihoods[-1] <= log_zero):
                        bond_color = red
                        anti_motif_list.append(h)
                    else:
                        #bond_color = (0, 255 * math.exp(-delta_l), 255 * (1 - math.exp(-delta_l)))
                        bond_color = green

                    motif_svg = chemconvert.hash2svg(h, 150, 150, black,
                                                     bond_color)
                    motif_svg.set_attribute("height", 200)
                    if (True):  # add
                        #motif_svg.add(svg.Text((35, 25), h, 12, green))
                        l_string = ",".join(
                            ["%.1f" % l for l in likelihoods[2:]])
                        motif_svg.add(
                            svg.Text((10, 160),
                                     "&#916;L = %.1f" % delta_l,
                                     font_size=12))
                        motif_svg.add(
                            svg.Text((10, 175), l_string, font_size=12))
                        if (count > 0):
                            #motif_svg.add(svg.Text((35, 75), "diff = %.1f" % (l1-l0), 12, black))
                            motif_svg.add(
                                svg.Text((10, 190),
                                         "count = %d" % count,
                                         font_size=12))
                        motif_svg.embed_in_html(template_html_file,
                                                motif_fullpath, h)
                    else:
                        template_html_file.write("<p>")
                        motif_svg.embed_in_html(template_html_file,
                                                motif_fullpath, h)
                        template_html_file.write("<a href=\"" + h + ".svg\">" +
                                                 h + "</a>")
                        template_html_file.write(", count = %d" % count)
                        for i in range(2, size + 1):
                            template_html_file.write(", L(%d) = %.1f" %
                                                     (i, likelihoods[i]))
                        template_html_file.write("</p>")
                template_html_file.close()
            else:
                size_html_file.write("No instances")

            size_html_file.write("</p>")
        size_html_file.close()
    main_html_file.close()

    util.write_text_file(anti_motif_list, "../results/stat/anti_motifs.txt")
    return