comparison jbrowse2.py @ 55:469c0f6d87d7 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 0553bb75a96ae401623face516c1cf6e1cfe743f

54:d6b0feb22584

                            fl = fls[1]
                            if len(fl.split()) > 1:
                                self.genome_firstcontig = fl.split()[0].strip()
                            else:
                                self.genome_firstcontig = fl
                        else:
                            fl = urrlib.request.urlopen(faname+".fai").readline()
                            if fl: # is first row of the text fai so the first contig name
                                self.genome_firstcontig = fl.decode('utf8').strip().split()[0]
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

        self.trackIdlist.append(tId)

    def add_cram(self, data, trackData, cram_index=None, **kwargs):
        tId = trackData["label"]
        useuri = trackData["useuri"].lower() == "yes"
        bindex = cram_index
        if useuri:
            url = data
        else:
            fname = "%s.cram" % trackData["label"]
            dest = "%s/%s" % (self.outdir, fname)
            bindex = fname + '.crai'
            url = fname
            self.subprocess_check_call(["cp", data, dest])
            if bindex is not None and os.path.exists(bindex):
                if not os.path.exists(dest+'.crai'):
                    # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
                    self.subprocess_check_call(
                        ["cp", os.path.realpath(cram_index), dest + ".crai"]
                    )

            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "CramAdapter",
                "cramLocation": {"uri": url},
                "craiLocation": {
                    "uri": bindex,
                },
                "sequenceAdapter": self.genome_sequence_adapter,
            },
            "displays": [
                {

        refName = None
        drdict = {
            "reversed": False,
            "assemblyName": self.genome_name,
            "start": 2000,
            "end": 0,
            "refName": "x",
        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]

55:469c0f6d87d7

                            fl = fls[1]
                            if len(fl.split()) > 1:
                                self.genome_firstcontig = fl.split()[0].strip()
                            else:
                                self.genome_firstcontig = fl
                    else:
                        fl = urllib.request.urlopen(fapath+".fai").readline()
                        if fl: # is first row of the text fai so the first contig name
                            self.genome_firstcontig = fl.decode('utf8').strip().split()[0]
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

        self.trackIdlist.append(tId)

    def add_cram(self, data, trackData, cram_index=None, **kwargs):
        tId = trackData["label"]
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            fname = "%s.cram" % trackData["label"]
            dest = "%s/%s" % (self.outdir, fname)
            url = fname
            self.subprocess_check_call(["cp", data, dest])
            if cram_index is not None and os.path.exists(cram_index):
                if not os.path.exists(dest+'.crai'):
                    # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
                    self.subprocess_check_call(
                        ["cp", os.path.realpath(cram_index), dest + ".crai"]
                    )

            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "CramAdapter",
                "cramLocation": {"uri": url},
                "craiLocation": {
                    "uri": url + '.crai',
                },
                "sequenceAdapter": self.genome_sequence_adapter,
            },
            "displays": [
                {

        refName = None
        drdict = {
            "reversed": False,
            "assemblyName": self.genome_name,
            "start": 2000,
            "end": 200000,
            "refName": "x",
        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]