def path_to_agp(g, path, object, sizes, status):
lines = []
for (a, ao), (b, bo) in pairwise(path):
ao = get_orientation(ao, status)
e = g.get_edge(a.v, b.v)
cline = AGPLine.cline(object, a.v, sizes, ao)
gline = AGPLine.gline(object, e.length)
lines.append(cline)
lines.append(gline)
# Do not forget the last one
z, zo = path[-1]
zo = get_orientation(zo, status)
cline = AGPLine.cline(object, z.v, sizes, zo)
lines.append(cline)
return lines
def path_to_agp(g, path, object, sizes, status):
lines = []
for (a, ao), (b, bo) in pairwise(path):
ao = get_orientation(ao, status)
e = g.get_edge(a.v, b.v)
cline = AGPLine.cline(object, a.v, sizes, ao)
gline = AGPLine.gline(object, e.length)
lines.append(cline)
lines.append(gline)
# Do not forget the last one
z, zo = path[-1]
zo = get_orientation(zo, status)
cline = AGPLine.cline(object, z.v, sizes, zo)
lines.append(cline)
return lines
def write_agp(self, filename):
sizes = self.sz
agp = []
for scaffold, lines in self.iter_scaffold():
for a, b in pairwise(lines):
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
gline = AGPLine.gline(scaffold, a.gaps)
agp.append(cline)
agp.append(gline)
a = lines[-1]
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
agp.append(cline)
fw = open(filename, "w")
for a in agp:
print >> fw, a
fw.close()
reindex([filename, "--inplace"])
return filename
def write_agp(self, filename):
sizes = self.sz
agp = []
for scaffold, lines in self.iter_scaffold():
for a, b in pairwise(lines):
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
gline = AGPLine.gline(scaffold, a.gaps)
agp.append(cline)
agp.append(gline)
a = lines[-1]
cline = AGPLine.cline(scaffold, a.tig, sizes, a.oo)
agp.append(cline)
fw = open(filename, "w")
for a in agp:
print >> fw, a
fw.close()
reindex([filename, "--inplace"])
return filename
