def run(self):
path_file = self.path_file
if isinstance(path_file, basestring):
t = BioPaxFile()
if path_file.endswith(".gz"):
handle = gzip.GzipFile(path_file)
t.load(handle)
else:
t.load(path_file)
path_file = t
paths = []
for key,value in path_file.pathways().iteritems():
add = False
if self.pathways is None or value in self.pathways:
add = True
elif key in self.pathways:
add = True
else:
a_name = re_namesplit.split(key)[-1]
if a_name in self.pathways:
add = True
if add:
paths.append(key)
for subnet in path_file.toNet(paths):
gr = networkx.MultiDiGraph()
for k, v in subnet.meta.items():
if k != 'type':
gr.graph[k] = v
subnet.to_graph(gr)
name = re_namesplit.split(gr.graph['url'])[-1]
if self.outdir is not None:
handle = open(os.path.join(self.outdir, name + ".xgmml"), "w")
elif self.singlepath is not None:
handle = open(self.singlepath, "w")
else:
handle = sys.stdout
convert.write_xgmml(gr, handle)
if self.singlepath is not None:
handle.close()
return
def run(self):
path_file = self.path_file
if isinstance(path_file, basestring):
t = BioPaxFile()
t.load(path_file)
path_file = t
paths = []
for key, value in path_file.pathways().iteritems():
add = False
if self.pathways is None or value in self.pathways:
add = True
elif key in self.pathways:
add = True
else:
a_name = re_namesplit.split(key)[-1]
if a_name in self.pathways:
add = True
if add:
paths.append(key)
for subnet in path_file.toNet(paths):
gr = networkx.MultiDiGraph()
for k, v in subnet.meta.items():
if k != 'type':
gr.graph[k] = v
subnet.to_graph(gr)
name = re_namesplit.split(gr.graph['url'])[-1]
if self.outdir is not None:
handle = open(os.path.join(self.outdir, name + ".xgmml"), "w")
elif self.singlepath is not None:
handle = open(self.singlepath, "w")
else:
handle = sys.stdout
convert.write_xgmml(gr, handle)
if self.singlepath is not None:
handle.close()
return
file_list = []
if args.sparql:
file_list = [ BioPaxSparql(args.input) ]
else:
for a in args.input:
if os.path.isdir(a):
file_list.extend(glob(os.path.join(a, "*")))
else:
file_list.append(a)
if args.list:
for path_file in file_list:
if isinstance(path_file, basestring):
t = BioPaxFile()
t.load(path_file)
path_file = t
for a,b in path_file.pathways().iteritems():
print a, b.encode('ascii', errors='ignore')
else:
if args.cpus > 1:
runs = []
for path_file in file_list:
runs.append( ConvertTask(path_file, args.out_dir, args.pathways) )
p = Pool(args.cpus)
p.map(runner, runs)
else:
for path_file in file_list:
ConvertTask(path_file, args.out_dir, args.pathways).run()
file_list = []
if args.sparql:
file_list = [BioPaxSparql(args.input)]
else:
for a in args.input:
if os.path.isdir(a):
file_list.extend(glob(os.path.join(a, "*")))
else:
file_list.append(a)
if args.list:
for path_file in file_list:
if isinstance(path_file, basestring):
t = BioPaxFile()
t.load(path_file)
path_file = t
for a, b in path_file.pathways().iteritems():
print a, b.encode('ascii', errors='ignore')
else:
if args.cpus > 1:
runs = []
for path_file in file_list:
runs.append(ConvertTask(path_file, args.out_dir,
args.pathways))
p = Pool(args.cpus)
p.map(runner, runs)
else:
for path_file in file_list:
