def merge(args):
"""
%prog merge graphs
Merge multiple graphs together and visualize.
"""
p = OptionParser(merge.__doc__)
p.add_option(
"--colorlist",
default="black,red,pink,blue,green",
help="The color palette",
)
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
colorlist = opts.colorlist.split(",")
assert len(colorlist) >= len(args), "Need more colors in --colorlist"
g = BiGraph()
for a, c in zip(args, colorlist):
g.read(a, color=c)
g.draw("merged.png")
def partition(args):
"""
%prog partition happy.txt synteny.graph
Select edges from another graph and merge it with the certain edges built
from the HAPPY mapping data.
"""
allowed_format = ("png", "ps")
p = OptionParser(partition.__doc__)
p.add_option("--prefix", help="Add prefix to the name [default: %default]")
p.add_option("--namestart", default=0, type="int",
help="Use a shorter name, starting index [default: %default]")
p.add_option("--format", default="png", choices=allowed_format,
help="Generate image of format [default: %default]")
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
happyfile, graphfile = args
bg = BiGraph()
bg.read(graphfile, color="red")
prefix = opts.prefix
fp = open(happyfile)
for i, row in enumerate(fp):
nns = happy_nodes(row, prefix=prefix)
nodes = set(nns)
edges = happy_edges(row, prefix=prefix)
small_graph = BiGraph()
for e, is_uncertain in edges:
if is_uncertain:
e.color = "gray"
small_graph.add_edge(e)
for (u, v), e in bg.edges.items():
# Grab edge if both vertices are on the same line
if u in nodes and v in nodes:
uv = (str(u), str(v))
if uv in small_graph.edges:
e = small_graph.edges[uv]
e.color = "blue" # supported by both evidences
else:
small_graph.add_edge(e)
print >> sys.stderr, small_graph
pngfile = "A{0:02d}.{1}".format(i + 1, opts.format)
telomeres = (nns[0], nns[-1])
small_graph.draw(pngfile, namestart=opts.namestart,
nodehighlight=telomeres, dpi=72)
legend = ["Edge colors:"]
legend.append("[BLUE] Experimental + Synteny")
legend.append("[BLACK] Experimental certain")
legend.append("[GRAY] Experimental uncertain")
legend.append("[RED] Synteny only")
legend.append("Rectangle nodes are telomeres.")
print >> sys.stderr, "\n".join(legend)
def merge(args):
"""
%prog merge graphs
Merge multiple graphs together and visualize.
"""
p = OptionParser(merge.__doc__)
p.add_option("--colorlist", default="black,red,pink,blue,green",
help="The color palette [default: %default]")
opts, args = p.parse_args(args)
if len(args) < 1:
sys.exit(not p.print_help())
colorlist = opts.colorlist.split(",")
assert len(colorlist) >= len(args), "Need more colors in --colorlist"
g = BiGraph()
for a, c in zip(args, colorlist):
g.read(a, color=c)
g.draw("merged.png")
def partition(args):
"""
%prog partition happy.txt synteny.graph
Select edges from another graph and merge it with the certain edges built
from the HAPPY mapping data.
"""
allowed_format = ("png", "ps")
p = OptionParser(partition.__doc__)
p.add_option("--prefix", help="Add prefix to the name")
p.add_option(
"--namestart",
default=0,
type="int",
help="Use a shorter name, starting index",
)
p.add_option(
"--format",
default="png",
choices=allowed_format,
help="Generate image of format",
)
opts, args = p.parse_args(args)
if len(args) != 2:
sys.exit(not p.print_help())
happyfile, graphfile = args
bg = BiGraph()
bg.read(graphfile, color="red")
prefix = opts.prefix
fp = open(happyfile)
for i, row in enumerate(fp):
nns = happy_nodes(row, prefix=prefix)
nodes = set(nns)
edges = happy_edges(row, prefix=prefix)
small_graph = BiGraph()
for (a, b, oa, ob), is_uncertain in edges:
color = "gray" if is_uncertain else "black"
small_graph.add_edge(a, b, oa, ob, color=color)
for (u, v), e in bg.edges.items():
# Grab edge if both vertices are on the same line
if u in nodes and v in nodes:
uv = (str(u), str(v))
if uv in small_graph.edges:
e = small_graph.edges[uv]
e.color = "blue" # supported by both evidences
else:
small_graph.add_edge(e)
print(small_graph, file=sys.stderr)
pngfile = "A{0:02d}.{1}".format(i + 1, opts.format)
telomeres = (nns[0], nns[-1])
small_graph.draw(
pngfile, namestart=opts.namestart, nodehighlight=telomeres, dpi=72
)
legend = [
"Edge colors:",
"[BLUE] Experimental + Synteny",
"[BLACK] Experimental certain",
"[GRAY] Experimental uncertain",
"[RED] Synteny only",
"Rectangle nodes are telomeres.",
]
print("\n".join(legend), file=sys.stderr)