comparison jbrowse2.py @ 68:c4eb6a85db70 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit bd958a96352bf8dbd1fdb5a2e994d57a42446f33-dirty

67:cefe9dbf1d80

                            )
                assmeta.append(this_genome)
        self.assemblies += assembly
        self.assmeta[genome_names[0]] = assmeta
        self.tracksToAdd[genome_names[0]] = []
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"] += assembly
        else:
            self.config_json["assemblies"] = assembly
        self.genome_names += genome_names
        return this_genome["genome_name"]

    def make_assembly(self, fapath, gname, useuri):
        if useuri:

        logging.debug(
            "### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s"
            % (pafOpts, pgnames, pgpaths, tId)
        )
        for i, gname in enumerate(pgnames):
            if len(gname.split()) > 1:
                gname = gname.split()[0]
            passnames.append(gname)
            # trouble from spacey names in command lines avoidance
            if gname not in self.genome_names:

                useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
                    "https://"
                )
                asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                self.genome_names.append(gname)
                if self.config_json.get("assemblies", None):
                    self.config_json["assemblies"].append(asstrack)
                else:
                    self.config_json["assemblies"] = [
                        asstrack,
                    ]
        lab = trackData["label"]
        url = "%s.paf" % (lab)
        dest = "%s/%s" % (self.outdir, url)
        self.symlink_or_copy(os.path.realpath(data), dest)
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,
            "assemblyNames": passnames,
            "category": [

                "type": "PAFAdapter",
                "pafLocation": {"uri": url},
                "assemblyNames": passnames,
            },
            "displays": [
                {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab},
                {
                    "type": "LinearComparativeDisplay",
                    "displayId": "%s-LinearComparativeDisplay" % lab,
                },
                {
                    "type": "LinearSyntenyDisplay",
                    "displayId": "%s-LinearSyntenyDisplay" % lab,
                },
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % lab,
                },
            ],
        }
        style_json = {
            "displays": [
                {
                    "type": "SyntenyDisplay",
                    "displayId": "%s-SyntenyDisplay" % lab,
                }
            ]
        }
        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)

                        "type": track_types[tId],
                        "configuration": tId,
                        "displays": [style_data],
                    }
                )
            # The view for the assembly we're adding
            view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
            refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
            drdict = {
                "reversed": False,
                "assemblyName": gnome,
                "start": 1,
                "end": 100000,
                "refName": refName
            }
            ddl = default_data.get("defaultLocation", None)
            if ddl:
                loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
                # allow commas like 100,000 but ignore as integer
                if loc_match:
                    refName = loc_match.group(1)
                    drdict["refName"] = refName
                    if loc_match.group(2) > "":
                        drdict["start"] = int(loc_match.group(2).replace(",", ""))
                    if loc_match.group(3) > "":
                        drdict["end"] = int(loc_match.group(3).replace(",", ""))
                else:
                    logging.info(
                        "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                        % ddl
                    )
            if drdict.get("refName", None):
                # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
                view_json["displayedRegions"] = [
                    drdict,
                ]
                logging.info("@@@ defaultlocation %s for default session" % drdict)
            else:
                logging.info(
                    "@@@ no contig name found for default session - please add one!"
                )
            session_views.append(view_json)
        session_name = default_data.get("session_name", "New session")
        for key, value in mapped_chars.items():
            session_name = session_name.replace(value, key)
        session_json["name"] = session_name

        "quaternary_color": root.find("metadata/general/quaternary_color").text,
        "font_size": root.find("metadata/general/font_size").text,
    }
    jc.add_general_configuration(general_data)
    trackconf = jc.config_json.get("tracks", [])
    for gnome in jc.genome_names:
        trackconf += jc.tracksToAdd[gnome]
    jc.config_json["tracks"] = trackconf
    jc.write_config()
    jc.add_default_session(default_session_data)
    # jc.text_index() not sure what broke here.

68:c4eb6a85db70

                            )
                assmeta.append(this_genome)
        self.assemblies += assembly
        self.assmeta[genome_names[0]] = assmeta
        self.tracksToAdd[genome_names[0]] = []
        self.genome_names += genome_names
        return this_genome["genome_name"]

    def make_assembly(self, fapath, gname, useuri):
        if useuri:

        logging.debug(
            "### add_paf got pafOpts=%s, pgnames=%s, pgpaths=%s for %s"
            % (pafOpts, pgnames, pgpaths, tId)
        )
        for i, gname in enumerate(pgnames):
            lab = trackData["label"]
            if len(gname.split()) > 1:
                gname = gname.split()[0]
            passnames.append(gname)
            # trouble from spacey names in command lines avoidance
            if gname not in self.genome_names:

                useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
                    "https://"
                )
                asstrack = self.make_assembly(pgpaths[i], gname, useuri)
                self.genome_names.append(gname)
                self.tracksToAdd[gname] = []
                self.assemblies.append(asstrack)
                if not useuri:
                    url = "%s.paf" % (lab)
                    dest = "%s/%s" % (self.outdir, url)
                    self.symlink_or_copy(os.path.realpath(data), dest)
                else:
                    url = data
        trackDict = {
            "type": "SyntenyTrack",
            "trackId": tId,
            "assemblyNames": passnames,
            "category": [

                "type": "PAFAdapter",
                "pafLocation": {"uri": url},
                "assemblyNames": passnames,
            },
            "displays": [
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % lab,
                },
                {"type": "DotplotDisplay", "displayId": "%s-DotplotDisplay" % lab},
                {
                    "type": "LinearComparativeDisplay",
                    "displayId": "%s-LinearComparativeDisplay" % lab,
                },
                {
                    "type": "LinearSyntenyDisplay",
                    "displayId": "%s-LinearSyntenyDisplay" % lab,
                },
            ],
        }
        style_json = {
            "displays": [
                {
                    "type": "LGVSyntenyDisplay",
                    "displayId": "%s-LGVSyntenyDisplay" % lab,
                }
            ]
        }
        trackDict["style"] = style_json
        self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)

                        "type": track_types[tId],
                        "configuration": tId,
                        "displays": [style_data],
                    }
                )
            # paf genomes have no tracks associated so nothing for the view
            if len(tracks_data) > 0:
                view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
                refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
                drdict = {
                    "reversed": False,
                    "assemblyName": gnome,
                    "start": 1,
                    "end": 100000,
                    "refName": refName
                }
                ddl = default_data.get("defaultLocation", None)
                if ddl:
                    loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
                    # allow commas like 100,000 but ignore as integer
                    if loc_match:
                        refName = loc_match.group(1)
                        drdict["refName"] = refName
                        if loc_match.group(2) > "":
                            drdict["start"] = int(loc_match.group(2).replace(",", ""))
                        if loc_match.group(3) > "":
                            drdict["end"] = int(loc_match.group(3).replace(",", ""))
                    else:
                        logging.info(
                            "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                            % ddl
                        )
                if drdict.get("refName", None):
                    # TODO displayedRegions is not just zooming to the region, it hides the rest of the chromosome
                    view_json["displayedRegions"] = [
                        drdict,
                    ]
                    logging.info("@@@ defaultlocation %s for default session" % drdict)
                else:
                    logging.info(
                        "@@@ no contig name found for default session - please add one!"
                    )
                session_views.append(view_json)
        session_name = default_data.get("session_name", "New session")
        for key, value in mapped_chars.items():
            session_name = session_name.replace(value, key)
        session_json["name"] = session_name

        "quaternary_color": root.find("metadata/general/quaternary_color").text,
        "font_size": root.find("metadata/general/font_size").text,
    }
    jc.add_general_configuration(general_data)
    trackconf = jc.config_json.get("tracks", [])
    logging.warn("genome_names=%s" % jc.genome_names)
    for gnome in jc.genome_names:
        trackconf += jc.tracksToAdd[gnome]
    jc.config_json["tracks"] = trackconf
    assconf = jc.config_json.get("assemblies", [])
    assconf += jc.assemblies
    jc.config_json["assemblies"] = assconf
    jc.write_config()
    jc.add_default_session(default_session_data)
    # jc.text_index() not sure what broke here.