def main_library_table(args): for path_dir in glob(os.path.join(args.library, "*")): if os.path.isdir(path_dir): path_name = os.path.basename(path_dir) xgmml_path = os.path.join(path_dir, "graph.xgmml") handle = open(xgmml_path) gr = network_convert.read_xgmml(handle) handle.close() organism = gr.graph.get('organism', '') name = gr.graph.get('displayName', None) if name is None: name = gr.graph.get('name', None) print "%s\t%s\t%s" % (path_name, organism, name)
def main_library_compile(args): builder = GraphBuilder(args) for path_dir in glob(os.path.join(args.library, "*")): if os.path.isdir(path_dir): path_name = os.path.basename(path_dir) xgmml_path = os.path.join(path_dir, "graph.xgmml") handle = open(xgmml_path) gr = network_convert.read_xgmml(handle) handle.close() fix_gr = builder.fix_graph(gr) spf_path = os.path.join(path_dir, "graph.spf") log("Writing: %s" % (spf_path)) handle = open(spf_path, "w") network_convert.write_spf(fix_gr, handle) handle.close()
def main_library_copy(args): builder = GraphBuilder(args) out_zip = zipfile.ZipFile(args.out, "w") out_base = re.sub( r'.zip$', '', os.path.basename(args.out)) for path_dir in glob(os.path.join(args.library, "*")): if os.path.isdir(path_dir): path_name = os.path.basename(path_dir) xgmml_path = os.path.join(path_dir, "graph.xgmml") handle = open(xgmml_path) gr = network_convert.read_xgmml(handle) handle.close() fix_gr = builder.fix_graph(gr) log("Writing: %s" % (path_name)) text = StringIO() network_convert.write_spf(fix_gr, text) if len(text.getvalue()) > 0: out_zip.writestr( os.path.join(out_base, path_name + ".spf"), text.getvalue()) out_zip.close()
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: if args.property in gr.node[node] and gr.node[node][args.property] in terms: found.append(node) if len(found):
def read(self): handle = open(self.path) cur_gr = network_convert.read_xgmml(handle) handle.close() return cur_gr
#!/usr/bin/env python import sys import argparse from pathway_tools import convert, biopax if __name__ == "__main__": parser = argparse.ArgumentParser() parser.add_argument('-o', "--output", default=None) parser.add_argument("input") args = parser.parse_args() handle = open(args.input) gr = convert.read_xgmml(handle) biopax.write_biopax(gr, sys.stdout)
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() if gr1 is None or gr2 is None: sys.stderr.write("Select files for source and dst graphs\n") sys.exit(1)
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: if args.target_nodetype is None or target_net.node[n][ 'type'] == args.target_nodetype: for pid in target_net.node[n][args.target_pathattr]: target_pathways[pid] = target_pathways.get(pid, 0) + 1
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: if args.target_nodetype is None or target_net.node[n]['type'] == args.target_nodetype: for pid in target_net.node[n][args.target_pathattr]: target_pathways[pid] = target_pathways.get(pid, 0) + 1