sbgn2sif

#!/usr/bin/env python3

# Copyright 2019-2020 Arnaud Poret

# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at

#     http://www.apache.org/licenses/LICENSE-2.0

# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import argparse
import os.path
import re
import xml.etree.ElementTree

parser=argparse.ArgumentParser(
description="""
Convert SBGN encoded pathways to the SIF file format.
""",
epilog="""
sbgn2sif is currently quite lazy. It only requires:
    * glyphs with IDs (in SBGN, glyphs are nodes)
    * glyphs with labels (i.e. node names)
    * arcs with IDs (in SBGN, arcs are edges)
    * arcs with classes (i.e. edge types)
    * arcs with valid source glyphs (cf. above)
    * arcs with valid target glyphs (cf. above)

If a glyph has more than one label then its name is the list of its labels
separated with "||".

If a SBGN file contains more than one map then they are processed independently.

XML namespace is ignored, if any.

For explanations about the SBGN file format see https://sbgn.github.io.

For explanations about the SIF file format see the readme file of sbgn2sif.
""",
formatter_class=argparse.RawDescriptionHelpFormatter
)
parser.add_argument("sbgnfile",type=str,metavar="<sbgnfile>",help="a SBGN encoded pathway",nargs="+")
args=parser.parse_args()

for sbgnFile in args.sbgnfile:
    #### OUT FILES #############################################################
    warnFile=list(os.path.splitext(sbgnFile))
    sifFile=list(os.path.splitext(sbgnFile))
    warnFile[1]=".warns.txt"
    sifFile[1]=".sif"
    warnFile="".join(warnFile)
    sifFile="".join(sifFile)
    #### LOCALS ################################################################
    warns=[]
    edges=[]
    maps=xml.etree.ElementTree.fromstring(re.sub(r"\bxmlns=\".*?\"","",open(sbgnFile,"rt").read())).findall("map")
    if len(maps)==0:
        print("Warning: "+sbgnFile+": no map(s)")
        continue
    #### MAPS ##################################################################
    for map_ in maps:
        glyphs={}
        arcs={}
        #### GLYPHS ############################################################
        for glyph in map_.findall("glyph"):
            id_=glyph.get("id")
            labels=glyph.findall("label")
            if (id_==None) or (id_.strip()==""):
                warns.append("glyph: no ID")
            elif id_ in glyphs.keys():
                warns.append("glyph: "+id_+": duplicated ID")
            elif len(labels)==0:
                warns.append("glyph: "+id_+": no label(s)")
            else:
                names=[]
                for label in labels:
                    name=label.get("text")
                    if (name==None) or (name.strip()==""):
                        warns.append("glyph: "+id_+": empty label")
                    elif name not in names:
                        names.append(name)
                if len(names)==0:
                    warns.append("glyph: "+id_+": no valid label(s)")
                else:
                    glyphs[id_]="||".join(names)
        if len(glyphs.keys())==0:
            warns.append("contains a map with no valid glyphs")
            continue
        #### PORTS #############################################################
        for glyph in map_.findall("glyph"):
            id_=glyph.get("id")
            if (id_!=None) and (id_ in glyphs.keys()):
                for port in glyph.findall("port"):
                    alias=port.get("id")
                    if (alias==None) or (alias.strip()==""):
                        warns.append("glyph: "+id_+": port: no ID")
                    elif alias in glyphs.keys():
                        warns.append("glyph: "+id_+": port: "+alias+": duplicated ID")
                    else:
                        glyphs[alias]=glyphs[id_]
        #### ARCS ##############################################################
        for arc in map_.findall("arc"):
            id_=arc.get("id")
            class_=arc.get("class")
            source=arc.get("source")
            target=arc.get("target")
            if (id_==None) or (id_.strip()==""):
                warns.append("arc: no ID")
            elif id_ in arcs.keys():
                warns.append("arc: "+id_+": duplicated ID")
            elif (class_==None) or (class_.strip()==""):
                warns.append("arc: "+id_+": no class")
            elif (source==None) or (source.strip()==""):
                warns.append("arc: "+id_+": no source glyph")
            elif (target==None) or (target.strip()==""):
                warns.append("arc: "+id_+": no target glyph")
            elif source not in glyphs.keys():
                warns.append("arc: "+id_+": "+source+": invalid or unknown source glyph")
            elif target not in glyphs.keys():
                warns.append("arc: "+id_+": "+target+": invalid or unknown target glyph")
            else:
                arcs[id_]="\t".join([glyphs[source],class_,glyphs[target]])
        if len(arcs.keys())==0:
            warns.append("contains a map with no valid arcs")
            continue
        #### EDGES #############################################################
        for id_ in arcs:
            if arcs[id_] not in edges:
                edges.append(arcs[id_])
    #### OUTPUTS ###############################################################
    if len(warns)!=0:
        print("Warning: "+sbgnFile+": see "+warnFile)
        open(warnFile,"w").write("\n".join(warns)+"\n")
    if len(edges)==0:
        print("Warning: "+sbgnFile+": no valid edges")
    else:
        open(sifFile,"w").write("\n".join(sorted(edges))+"\n")