Example #1
0
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)
Example #2
0
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()
Example #3
0
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()
Example #4
0
            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):
Example #5
0
 def read(self):
     handle = open(self.path)
     cur_gr = network_convert.read_xgmml(handle)
     handle.close()
     return cur_gr
Example #6
0
#!/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)
Example #7
0
    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)
Example #8
0
    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