def main_library_gmt(args):
filter_map = None
if args.filter is not None:
filter_map = {}
handle = open(args.filter)
for line in handle:
filter_map[line.rstrip()] = True
handle.close()
for path_dir in glob(os.path.join(args.library, "*")):
if os.path.isdir(path_dir):
path_name = os.path.basename(path_dir)
spf_path = os.path.join(path_dir, "graph.spf")
handle = open(spf_path)
gr = network_convert.read_spf(handle, strict=False)
handle.close()
if args.organism is None or gr.graph.get('organism', args.organism) == args.organism:
if filter_map is None:
out = gr.node.keys()
else:
out = []
for a in gr.node.keys():
if a in filter_map:
out.append(a)
if not args.skip_empty or len(out):
print "%s\t%s" % (path_name, "\t".join(out))
def check_project(self, project):
handle = open(os.path.join(self.repo, project, "INFO"))
conf = yaml.load(handle.read())
handle.close()
errors = []
if 'PID' not in conf:
errors.append(Exception("Missing required PID field"))
if 'DESC' not in conf:
errors.append(Exception("Missing required DESC description field"))
if 'SOURCE' not in conf:
errors.append(Exception("Missing required SOURCE field"))
handle = open(os.path.join(self.repo, project, "graph"))
gr = network_convert.read_spf(handle)
handle.close()
if self.hugo_map is not None:
for node in gr.node:
if gr.node[node]['type'] == 'protein':
if node not in self.hugo_map:
errors.append(Exception("Gene Symbol not found:\t%s" % (node)))
if self.dogma is not None:
for node in gr.node:
ntype = gr.node[node]['type']
if self.dogma.get_dogma(ntype) == None:
errors.append(Exception("No dogma for node %s type %s" % (node, ntype)))
return errors
paths = None
if args.r:
paths = []
for a in start_paths:
paths += list(scan_dir(a, args.filter))
else:
paths = start_paths
for file_path in paths:
gr = None
if args.spf:
handle = open(file_path)
gr = network_convert.read_spf(handle, strict=False)
handle.close()
else:
handle = open(file_path)
gr = network_convert.read_xgmml(handle)
handle.close()
if gr is not None:
found = []
if args.property is None:
for t in terms:
if t in gr.node:
found = [ t ]
else:
for node in gr.node:
def read(self):
handle = open(self.path)
cur_gr = network_convert.read_spf(handle, strict=False)
handle.close()
return cur_gr
def maxCC(ccs):
max = 0
for cc in ccs:
if len(cc) > max:
max = len(cc)
return max
graph = None
if opts.network.endswith(".sif"):
graph = convert.read_sif(open(opts.network))
else:
graph = convert.read_spf(open(opts.network))
heats = parseHeats(opts.heats)
if opts.cut_graph and not opts.node_attributes:
cut_val = None
try:
cutoff = float(opts.cut_graph)
except:
raise Exception(
"Error: value supplied to cut_graph must be a positive number")
cutG = cutGraph(graph, heats, cutoff)
convert.write_sif(cutG, sys.stdout)
sys.exit(0)
if opts.node_attributes:
#!/usr/bin/env python
import sys
import os
from pathway_tools import convert
import yaml
if __name__ == "__main__":
handle = open(sys.argv[1])
gr = convert.read_spf(handle, strict=False)
handle.close()
name_tab = {}
handle = open(sys.argv[2])
for line in handle:
tmp = line.rstrip().split("\t")
name_tab[tmp[0]] = tmp[1:]
outdir = sys.argv[3]
i = 1
for pathid in name_tab:
print pathid
pathdir = os.path.join(outdir, pathid)
if not os.path.exists(pathdir):
os.mkdir(pathdir)
config = {"DESC" : str(pathid)}
#if path in name_tab:
# config["PID"] = int(name_tab[path][0])
# config["SOURCE"] = str(name_tab[path][1])
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('--src-spf', help="Source SimplePathwayFile")
parser.add_argument('--dst-spf', help="Dest SimplePathwayFile")
parser.add_argument('--src-xgmml', help="Source XGMML File")
parser.add_argument('--dst-xgmml', help="Dest XGMML File")
args = parser.parse_args()
gr1 = None
gr2 = None
if args.src_spf:
handle1 = open(args.src_spf)
gr1 = network_convert.read_spf(handle1, strict=False)
handle1.close()
if args.src_xgmml:
handle1 = open(args.src_xgmml)
gr1 = network_convert.read_xgmml(handle1)
handle1.close()
if args.dst_spf:
handle2 = open(args.dst_spf)
gr2 = network_convert.read_spf(handle2, strict=False)
handle2.close()
if args.src_xgmml:
handle1 = open(args.dst_xgmml)
gr2 = network_convert.read_xgmml(handle1)
handle1.close()
default=None)
parser.add_argument('--target-xgmml',
help="Search Target in XGMML graph format",
default=None)
parser.add_argument('--query-pathattr', default="pid")
parser.add_argument('--target-pathattr', default="pid")
parser.add_argument("--query-nodetype", default=None)
parser.add_argument("--target-nodetype", default=None)
parser.add_argument("--min", "-m", type=int, default=1)
parser.add_argument("--top", type=int, default=None)
args = parser.parse_args()
if args.query_spf:
handle = open(args.query_spf)
query_net = convert.read_spf(handle)
if args.query_xgmml:
handle = open(args.query_xgmml)
query_net = convert.read_xgmml(handle)
if args.target_spf:
handle = open(args.target_spf)
target_net = convert.read_spf(handle)
if args.target_xgmml:
handle = open(args.target_xgmml)
target_net = convert.read_xgmml(handle)
target_pathways = {}
for n in target_net.node:
import networkx
from pathway_tools import convert
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('--spf', help="SimplePathwayFormat File")
parser.add_argument('--xgmml', help="XGMML File")
parser.add_argument('--top', help="Top Count", type=int, default=10)
args = parser.parse_args()
gr = None
if args.spf:
handle = open(args.spf)
gr = convert.read_spf(handle, strict=False)
handle.close()
if args.xgmml:
handle = open(args.xgmml)
gr = convert.read_xgmml(handle)
handle.close()
type_count = {}
for node in gr.node:
if 'type' in gr.node[node]:
node_type = gr.node[node]['type']
type_count[node_type] = type_count.get(node_type, 0) + 1
print("Node Count: %d" % (len(gr.nodes())))
print("Edge Count: %d" % (len(gr.edges())))
print("Connected Components: %d" %
return nodes
def maxCC(ccs):
max = 0
for cc in ccs:
if len(cc) > max:
max = len(cc)
return max
graph = None
if opts.network.endswith(".sif"):
graph = convert.read_sif(open(opts.network))
else:
graph = convert.read_spf(open(opts.network))
heats = parseHeats(opts.heats)
if opts.cut_graph and not opts.node_attributes:
cut_val = None
try:
cutoff = float(opts.cut_graph)
except:
raise Exception("Error: value supplied to cut_graph must be a positive number")
cutG = cutGraph(graph, heats, cutoff)
convert.write_sif(cutG, sys.stdout)
sys.exit(0)
if opts.node_attributes:
if not opts.cut_graph:
parser.add_argument('--query-spf', help="Input query in simple pathway format", default=None)
parser.add_argument('--query-xgmml', help="Input query in XGMML graph format", default=None)
parser.add_argument('--target-sfp', help="Search Target in Simple Pathway Format", default=None)
parser.add_argument('--target-xgmml', help="Search Target in XGMML graph format", default=None)
parser.add_argument('--query-pathattr', default="pid")
parser.add_argument('--target-pathattr', default="pid")
parser.add_argument("--query-nodetype", default=None)
parser.add_argument("--target-nodetype", default=None)
parser.add_argument("--min", "-m", type=int, default=1)
parser.add_argument("--top", type=int, default=None)
args = parser.parse_args()
if args.query_spf:
handle = open(args.query_spf)
query_net = convert.read_spf(handle)
if args.query_xgmml:
handle = open(args.query_xgmml)
query_net = convert.read_xgmml(handle)
if args.target_spf:
handle = open(args.target_spf)
target_net = convert.read_spf(handle)
if args.target_xgmml:
handle = open(args.target_xgmml)
target_net = convert.read_xgmml(handle)
target_pathways = {}
