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, must be one of {0}".\
format("|".join(allowed_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)
from jcvi.utils.table import banner
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, banner(legend)
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, must be one of {0}".\
format("|".join(allowed_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)
from jcvi.utils.table import banner
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, banner(legend)
