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()
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()
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), "ΔL = %.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
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),
"ΔL = %.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