comparison jbrowse2.py @ 46:4181e97c70a7 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a

45:0ec526d2d8c1

import re
import shutil
import struct
import subprocess
import tempfile
import xml.etree.ElementTree as ET
from collections import defaultdict

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")

            ]
        }

    def process_genomes(self):
        assemblies = []
        for i, genome_node in enumerate(self.genome_paths):
            genome_name = genome_node["meta"]["dataset_dname"].strip()
            if len(genome_name.split()) > 1:
                genome_name = genome_name.split()[0]
                # spaces and cruft break scripts when substituted
            if genome_name not in self.genome_names:
                # ignore dupes - can have multiple pafs with same references?
                fapath = genome_node["path"]
                assem = self.make_assembly(fapath, genome_name)
                assemblies.append(assem)
                self.genome_names.append(genome_name)
                if self.genome_name is None:
                    self.genome_name = (
                        genome_name  # first one for all tracks - other than paf
                    )
                    self.genome_firstcontig = None
                    fl = open(fapath, "r").readline().strip().split(">")
                    if len(fl) > 1:
                        fl = fl[1]
                        if len(fl.split()) > 1:
                            self.genome_firstcontig = fl.split()[0].strip()
                        else:
                            self.genome_firstcontig = fl
        if self.config_json.get("assemblies", None):
            self.config_json["assemblies"] += assemblies
        else:
            self.config_json["assemblies"] = assemblies

    def make_assembly(self, fapath, gname):

        faname = gname + ".fa.gz"
        fadest = os.path.realpath(os.path.join(self.outdir, faname))
        cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
            fapath,
            fadest,
            fadest,
            fadest,
        )
        self.subprocess_popen(cmd)
        adapter = {
            "type": "BgzipFastaAdapter",
            "fastaLocation": {
                "uri": faname,
            },
            "faiLocation": {
                "uri": faname + ".fai",
            },
            "gziLocation": {
                "uri": faname + ".gzi",
            },
        }
        self.genome_sequence_adapter = adapter
        trackDict = {
            "name": gname,
            "sequence": {
                "type": "ReferenceSequenceTrack",

        ]
        self.subprocess_check_call(cmd)

    def write_config(self):
        with open(self.config_json_file, "w") as fp:
            json.dump(self.config_json, fp)

    def text_index(self):
        # Index tracks
        args = [
            "jbrowse",

        """
        tId = trackData["label"]
        # can be served - if public.
        # dsId = trackData["metadata"]["dataset_id"]
        # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
        hname = trackData["hic_url"]
        floc = {
            "uri": hname,
        }
        trackDict = {
            "type": "HicTrack",
            "trackId": tId,
            "name": hname,
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "HicAdapter",
                "hicLocation": floc,
            },
            "displays": [
                {
                    "type": "LinearHicDisplay",
                    "displayId": "%s-LinearHicDisplay" % tId,

        from https://github.com/cmdcolin/maf2bed
        Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name
        e.g. hg38.chr1 in the sequence identifiers.
        need the reference id - eg hg18, for maf2bed.pl as the first parameter
        """
        mafPlugin = {
            "plugins": [
                {
                    "name": "MafViewer",
                    "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
                }
            ]
        }
        tId = trackData["label"]
        fname = "%s.bed" % tId
        dest = "%s/%s" % (self.outdir, fname)
        gname = self.genome_name
        cmd = [
            "bash",

        "resolution": 1,
        "posColor": "rgb(228, 26, 28)",
        "negColor": "rgb(255, 255, 51)",
        "constraints": {}
        """
        url = "%s.bigwig" % trackData["label"]
        # slashes in names cause path trouble
        dest = os.path.join(self.outdir, url)
        cmd = ["cp", data, dest]
        self.subprocess_check_call(cmd)
        bwloc = {"uri": url}
        tId = trackData["label"]
        trackDict = {
            "type": "QuantitativeTrack",
            "trackId": tId,

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_bam(self, data, trackData, bamOpts, bam_index=None, **kwargs):
        tId = trackData["label"]
        fname = "%s.bam" % trackData["label"]
        dest = "%s/%s" % (self.outdir, fname)
        url = fname
        self.subprocess_check_call(["cp", data, dest])
        bloc = {"uri": url}
        if bam_index is not None and os.path.exists(os.path.realpath(bam_index)):
            # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
            self.subprocess_check_call(
                ["cp", os.path.realpath(bam_index), dest + ".bai"]
            )
        else:
            # Can happen in exotic condition
            # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
            #      => no index generated by galaxy, but there might be one next to the symlink target
            #      this trick allows to skip the bam sorting made by galaxy if already done outside
            if os.path.exists(os.path.realpath(data) + ".bai"):
                self.symlink_or_copy(os.path.realpath(data) + ".bai", dest + ".bai")
            else:
                log.warn("Could not find a bam index (.bai file) for %s", data)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "BamAdapter",
                "bamLocation": bloc,
                "index": {
                    "location": {
                        "uri": fname + ".bai",
                    }
                },
            },
            "displays": [
                {

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_cram(self, data, trackData, cramOpts, cram_index=None, **kwargs):
        tId = trackData["label"]
        fname = "%s.cram" % trackData["label"]
        dest = "%s/%s" % (self.outdir, fname)
        url = fname
        self.subprocess_check_call(["cp", data, dest])
        bloc = {"uri": url}
        if cram_index is not None and os.path.exists(os.path.realpath(cram_index)):
            # 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"]
            )
        else:
            # Can happen in exotic condition
            # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
            #      => no index generated by galaxy, but there might be one next to the symlink target
            #      this trick allows to skip the bam sorting made by galaxy if already done outside
            if os.path.exists(os.path.realpath(data) + ".crai"):
                self.symlink_or_copy(os.path.realpath(data) + ".crai", dest + ".crai")
            else:
                log.warn("Could not find a cram index (.crai file) for %s", data)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "CramAdapter",
                "cramLocation": bloc,
                "craiLocation": {
                    "uri": fname + ".crai",
                },
                "sequenceAdapter": self.genome_sequence_adapter,
            },
            "displays": [
                {

        tId = trackData["label"]
        # url = "%s/api/datasets/%s/display" % (
        # self.giURL,
        # trackData["metadata"]["dataset_id"],
        # )
        url = "%s.vcf.gz" % tId
        dest = "%s/%s" % (self.outdir, url)
        cmd = "bgzip -c %s  > %s" % (data, dest)
        self.subprocess_popen(cmd)
        cmd = ["tabix", "-f", "-p", "vcf", dest]
        self.subprocess_check_call(cmd)
        trackDict = {
            "type": "VariantTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "VcfTabixAdapter",
                "vcfGzLocation": {
                    "uri": url,
                },
                "index": {
                    "location": {
                        "uri": url + ".tbi",
                    }

        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def _sort_gff(self, data, dest):
        # Only index if not already done
        if not os.path.exists(dest + ".gz"):
            cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s.gz'" % (
                data,
                dest,
            )  # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'"
            self.subprocess_popen(cmd)
            self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest + ".gz"])

    def _sort_bed(self, data, dest):
        # Only index if not already done
        if not os.path.exists(dest):
            cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest)
            self.subprocess_popen(cmd)
            cmd = ["tabix", "-f", "-p", "bed", dest]
            self.subprocess_check_call(cmd)

    def add_gff(self, data, ext, trackData):
        url = "%s.%s" % (trackData["label"], ext)
        dest = "%s/%s" % (self.outdir, url)
        self._sort_gff(data, dest)
        url = url + ".gz"
        tId = trackData["label"]
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],

        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_bed(self, data, ext, trackData):
        url = "%s.%s" % (trackData["label"], ext)
        dest = "%s/%s.gz" % (self.outdir, url)
        self._sort_bed(data, dest)
        tId = trackData["label"]
        url = url + ".gz"
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],

    def process_annotations(self, track):
        category = track["category"].replace("__pd__date__pd__", TODAY)
        for i, (
            dataset_path,
            dataset_ext,
            track_human_label,
            extra_metadata,
        ) in enumerate(track["trackfiles"]):
            # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
            for key, value in mapped_chars.items():
                track_human_label = track_human_label.replace(value, key)
            track_human_label = track_human_label.replace(" ", "_")
            outputTrackConfig = {
                "category": category,
                "style": {},
            }

            outputTrackConfig["key"] = track_human_label

            outputTrackConfig["trackset"] = track.get("trackset", {})
            outputTrackConfig["label"] = "%s_%i_%s" % (
                dataset_ext,
                i,

                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext == "bam":
                real_indexes = track["conf"]["options"]["bam"]["bam_index"]
                if not isinstance(real_indexes, list):
                    real_indexes = [real_indexes]

                self.add_bam(
                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["bam"],
                    bam_index=real_indexes[i],
                )
            elif dataset_ext == "cram":
                real_indexes = track["conf"]["options"]["cram"][ "cram_index"]
                if not isinstance(real_indexes, list):
                    real_indexes = [real_indexes]

                self.add_cram(
                    dataset_path,
                    outputTrackConfig,
                    track["conf"]["options"]["cram"],
                    cram_index=real_indexes[i],
                )
            elif dataset_ext == "blastxml":
                self.add_blastxml(
                    dataset_path,
                    outputTrackConfig,

        drdict = {
            "reversed": False,
            "assemblyName": self.genome_name,
            "start": 0,
            "end": 100000,
        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]
            loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)

        self.config_json.update(config_json)
        with open(config_path, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now """
        dest = self.outdir
        #self.subprocess_check_call(['jbrowse', 'create', dest, '--tag', f"{JB_VER}"])
        shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--xml", help="Track Configuration")
    parser.add_argument("--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda")
    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()

    jc = JbrowseConnector(
        outdir=args.outdir,
        jbrowse2path=args.jbrowse2path,
        genomes=[
            {
                "path": os.path.realpath(x.attrib["path"]),
                "meta": metadata_from_node(x.find("metadata")),
            }
            for x in root.findall("metadata/genomes/genome")
        ],
    )

            pass

        trackfiles = track.findall("files/trackFile")
        if trackfiles:
            for x in track.findall("files/trackFile"):
                if is_multi_bigwig:
                    multi_bigwig_paths.append(
                        (
                            x.attrib["label"],
                            os.path.realpath(x.attrib["path"]),
                        )
                    )
                else:
                    if trackfiles:
                        metadata = metadata_from_node(x.find("metadata"))
                        track_conf["dataset_id"] = metadata["dataset_id"]
                        track_conf["trackfiles"].append(
                            (
                                os.path.realpath(x.attrib["path"]),
                                x.attrib["ext"],
                                x.attrib["label"],
                                metadata,
                            )
                        )

        if is_multi_bigwig:
            metadata = metadata_from_node(x.find("metadata"))

            track_conf["trackfiles"].append(

            # Only pertains to gff3 + blastxml. TODO?
            track_conf["style"] = {t.tag: t.text for t in track.find("options/style")}
        except TypeError:
            track_conf["style"] = {}
            pass
        track_conf["conf"] = etree_to_dict(track.find("options"))
        keys = jc.process_annotations(track_conf)

        if keys:
            for key in keys:
                default_session_data["visibility"][

46:4181e97c70a7

import re
import shutil
import struct
import subprocess
import tempfile
import urllib.request
import xml.etree.ElementTree as ET
from collections import defaultdict

logging.basicConfig(level=logging.INFO)
log = logging.getLogger("jbrowse")

            ]
        }

    def process_genomes(self):
        assemblies = []
        useuri = False
        for i, genome_node in enumerate(self.genome_paths):
            if genome_node["useuri"].strip().lower() == "yes":
                useuri = True
            genome_name = genome_node["meta"]["dataset_dname"].strip()
            if len(genome_name.split()) > 1:
                genome_name = genome_name.split()[0]
                # spaces and cruft break scripts when substituted
            if genome_name not in self.genome_names:
                # ignore dupes - can have multiple pafs with same references?
                fapath = genome_node["path"]
                if not useuri:
                    fapath = os.path.realpath(fapath)
                assem = self.make_assembly(fapath, genome_name, useuri)
                assemblies.append(assem)
                self.genome_names.append(genome_name)
                if self.genome_name is None:
                    self.genome_name = (
                        genome_name  # first one for all tracks - other than paf
                    )
                    self.genome_firstcontig = None
                    if not useuri:
                        # https://lazarus.name/jbrowse/fish/bigwig_0_coverage_bedgraph_cov_count_count_bw.bigwig
                        # https://lazarus.name/jbrowse/fish/klBraLanc5.haps_combined.decontam.20230620.fasta.fa.gz
                        fl = open(fapath, "r").readline()
                        fls = fl.strip().split(">")
                        if len(fls) > 1:
                            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

    def make_assembly(self, fapath, gname, useuri):
        if useuri:
            faname = fapath
            adapter = {
                "type": "BgzipFastaAdapter",
                "fastaLocation": {
                    "uri": faname,
                    "locationType": "UriLocation",
                },
                "faiLocation": {
                    "uri": faname + ".fai",
                    "locationType": "UriLocation",
                },
                "gziLocation": {
                    "uri": faname + ".gzi",
                    "locationType": "UriLocation",
                },
            }
        else:
            faname = gname + ".fa.gz"
            fadest = os.path.realpath(os.path.join(self.outdir, faname))
            cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % (
                fapath,
                fadest,
                fadest,
                fadest,
            )
            self.subprocess_popen(cmd)

            adapter = {
                "type": "BgzipFastaAdapter",
                "fastaLocation": {
                    "uri": faname,
                },
                "faiLocation": {
                    "uri": faname + ".fai",
                },
                "gziLocation": {
                    "uri": faname + ".gzi",
                },
            }
        self.genome_sequence_adapter = adapter
        trackDict = {
            "name": gname,
            "sequence": {
                "type": "ReferenceSequenceTrack",

        ]
        self.subprocess_check_call(cmd)

    def write_config(self):
        with open(self.config_json_file, "w") as fp:
            json.dump(self.config_json, fp, indent=2)

    def text_index(self):
        # Index tracks
        args = [
            "jbrowse",

        """
        tId = trackData["label"]
        # can be served - if public.
        # dsId = trackData["metadata"]["dataset_id"]
        # url = "%s/api/datasets/%s/display?to_ext=hic " % (self.giURL, dsId)
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            uri = data
        else:
            uri = trackData["hic_url"]
        trackDict = {
            "type": "HicTrack",
            "trackId": tId,
            "name": uri,
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "HicAdapter",
                "hicLocation": uri,
            },
            "displays": [
                {
                    "type": "LinearHicDisplay",
                    "displayId": "%s-LinearHicDisplay" % tId,

        from https://github.com/cmdcolin/maf2bed
        Note: Both formats start with a MAF as input, and note that your MAF file should contain the species name and chromosome name
        e.g. hg38.chr1 in the sequence identifiers.
        need the reference id - eg hg18, for maf2bed.pl as the first parameter
        """
        tId = trackData["label"]
        mafPlugin = {
            "plugins": [
                {
                    "name": "MafViewer",
                    "url": "https://unpkg.com/jbrowse-plugin-mafviewer/dist/jbrowse-plugin-mafviewer.umd.production.min.js",
                }
            ]
        }

        fname = "%s.bed" % tId
        dest = "%s/%s" % (self.outdir, fname)
        gname = self.genome_name
        cmd = [
            "bash",

        "resolution": 1,
        "posColor": "rgb(228, 26, 28)",
        "negColor": "rgb(255, 255, 51)",
        "constraints": {}
        """
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = "%s.bigwig" % trackData["label"]
            # slashes in names cause path trouble
            dest = os.path.join(self.outdir, url)
            cmd = ["cp", data, dest]
            self.subprocess_check_call(cmd)
        bwloc = {"uri": url}
        tId = trackData["label"]
        trackDict = {
            "type": "QuantitativeTrack",
            "trackId": tId,

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_bam(self, data, trackData, bam_index=None, **kwargs):
        tId = trackData["label"]
        useuri = trackData["useuri"].lower() == "yes"
        bindex = bam_index
        if useuri:
            url = data
        else:
            fname = "%s.bam" % trackData["label"]
            dest = "%s/%s" % (self.outdir, fname)
            url = fname
            bindex = fname + '.bai'
            self.subprocess_check_call(["cp", data, dest])
            if bam_index is not None and os.path.exists(bam_index):
                if not os.path.exists(bindex):
                    # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
                    self.subprocess_check_call(
                        ["cp", bam_index, bindex]
                    )
                else:
                    # Can happen in exotic condition
                    # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
                    #      => no index generated by galaxy, but there might be one next to the symlink target
                    #      this trick allows to skip the bam sorting made by galaxy if already done outside
                    if os.path.exists(os.path.realpath(data) + ".bai"):
                        self.symlink_or_copy(os.path.realpath(data) + ".bai", bindex)
                    else:
                        log.warn("Could not find a bam index (.bai file) for %s", data)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "BamAdapter",
                "bamLocation": {"uri": url},
                "index": {
                    "location": {
                        "uri": bindex,
                    }
                },
            },
            "displays": [
                {

        style_json = self._prepare_track_style(trackDict)
        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        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 + '.bai'
            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"]
                    )
                else:
                    # Can happen in exotic condition
                    # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
                    #      => no index generated by galaxy, but there might be one next to the symlink target
                    #      this trick allows to skip the bam sorting made by galaxy if already done outside
                    if os.path.exists(os.path.realpath(data) + ".crai"):
                        self.symlink_or_copy(
                            os.path.realpath(data) + ".crai", dest + ".crai"
                        )
                    else:
                        log.warn("Could not find a cram index (.crai file) for %s", data)
        trackDict = {
            "type": "AlignmentsTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "CramAdapter",
                "cramLocation": {"uri": url},
                "craiLocation": {
                    "uri": bindex,
                },
                "sequenceAdapter": self.genome_sequence_adapter,
            },
            "displays": [
                {

        tId = trackData["label"]
        # url = "%s/api/datasets/%s/display" % (
        # self.giURL,
        # trackData["metadata"]["dataset_id"],
        # )

        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = "%s.vcf.gz" % tId
            dest = "%s/%s" % (self.outdir, url)
            cmd = "bgzip -c %s  > %s" % (data, dest)
            self.subprocess_popen(cmd)
            cmd = ["tabix", "-f", "-p", "vcf", dest]
            self.subprocess_check_call(cmd)
        trackDict = {
            "type": "VariantTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],
            "adapter": {
                "type": "VcfTabixAdapter",
                "vcfGzLocation": {
                    "uri": url
                },
                "index": {
                    "location": {
                        "uri": url + ".tbi",
                    }

        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def _sort_gff(self, data, dest):
        # Only index if not already done
        if not os.path.exists(dest):
            cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % (
                data,
                dest,
            )  # "gff3sort.pl --precise '%s' | grep -v \"^$\" > '%s'"
            self.subprocess_popen(cmd)
            self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])

    def _sort_bed(self, data, dest):
        # Only index if not already done
        if not os.path.exists(dest):
            cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest)
            self.subprocess_popen(cmd)
            cmd = ["tabix", "-f", "-p", "bed", dest]
            self.subprocess_check_call(cmd)

    def add_gff(self, data, ext, trackData):
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = trackData["path"]
        else:
            url = "%s.%s.gz" % (trackData["label"], ext)
            dest = "%s/%s" % (self.outdir, url)
            self._sort_gff(data, dest)
        tId = trackData["label"]
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],

        trackDict["style"] = style_json
        self.tracksToAdd.append(trackDict)
        self.trackIdlist.append(tId)

    def add_bed(self, data, ext, trackData):
        tId = trackData["label"]
        useuri = trackData["useuri"].lower() == "yes"
        if useuri:
            url = data
        else:
            url = "%s.%s.gz" % (trackData["label"], ext)
            dest = "%s/%s" % (self.outdir, url)
            self._sort_bed(data, dest)
        trackDict = {
            "type": "FeatureTrack",
            "trackId": tId,
            "name": trackData["name"],
            "assemblyNames": [self.genome_name],

    def process_annotations(self, track):
        category = track["category"].replace("__pd__date__pd__", TODAY)
        for i, (
            dataset_path,
            dataset_ext,
            useuri,
            track_human_label,
            extra_metadata,
        ) in enumerate(track["trackfiles"]):
            if not dataset_path.strip().startswith("http"):
                # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
                for key, value in mapped_chars.items():
                    track_human_label = track_human_label.replace(value, key)
                track_human_label = track_human_label.replace(" ", "_")
            outputTrackConfig = {
                "category": category,
                "style": {},
            }

            outputTrackConfig["key"] = track_human_label
            outputTrackConfig["useuri"] = useuri

            outputTrackConfig["trackset"] = track.get("trackset", {})
            outputTrackConfig["label"] = "%s_%i_%s" % (
                dataset_ext,
                i,

                    dataset_path,
                    outputTrackConfig,
                )
            elif dataset_ext == "bam":
                real_indexes = track["conf"]["options"]["bam"]["bam_index"]
                self.add_bam(
                    dataset_path,
                    outputTrackConfig,
                    bam_index=real_indexes,
                )
            elif dataset_ext == "cram":
                real_indexes = track["conf"]["options"]["cram"]["cram_index"]
                self.add_cram(
                    dataset_path,
                    outputTrackConfig,
                    cram_index=real_indexes,
                )
            elif dataset_ext == "blastxml":
                self.add_blastxml(
                    dataset_path,
                    outputTrackConfig,

        drdict = {
            "reversed": False,
            "assemblyName": self.genome_name,
            "start": 0,
            "end": 100000,
            "refName": "x",
        }

        if data.get("defaultLocation", ""):
            ddl = data["defaultLocation"]
            loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)

        self.config_json.update(config_json)
        with open(config_path, "w") as config_file:
            json.dump(self.config_json, config_file, indent=2)

    def clone_jbrowse(self):
        """Clone a JBrowse directory into a destination directory. This also works in Biocontainer testing now"""
        dest = self.outdir
        # self.subprocess_check_call(['jbrowse', 'create', dest, '--tag', f"{JB_VER}"])
        shutil.copytree(self.jbrowse2path, dest, dirs_exist_ok=True)
        for fn in [
            "asset-manifest.json",
            "favicon.ico",
            "robots.txt",

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--xml", help="Track Configuration")
    parser.add_argument(
        "--jbrowse2path", help="Path to JBrowse2 directory in biocontainer or Conda"
    )
    parser.add_argument("--outdir", help="Output directory", default="out")
    parser.add_argument("--version", "-V", action="version", version="%(prog)s 2.0.1")
    args = parser.parse_args()
    tree = ET.parse(args.xml)
    root = tree.getroot()

    jc = JbrowseConnector(
        outdir=args.outdir,
        jbrowse2path=args.jbrowse2path,
        genomes=[
            {
                "path": x.attrib["path"],
                "label": x.attrib["label"],
                "useuri": x.attrib["useuri"],
                "meta": metadata_from_node(x.find("metadata")),
            }
            for x in root.findall("metadata/genomes/genome")
        ],
    )

            pass

        trackfiles = track.findall("files/trackFile")
        if trackfiles:
            for x in track.findall("files/trackFile"):
                track_conf["useuri"] = x.attrib["useuri"]
                if is_multi_bigwig:
                    multi_bigwig_paths.append(
                        (
                            x.attrib["label"],
                            x.attrib["useuri"],
                            os.path.realpath(x.attrib["path"]),
                        )
                    )
                else:
                    if trackfiles:
                        metadata = metadata_from_node(x.find("metadata"))
                        track_conf["dataset_id"] = metadata["dataset_id"]
                        if x.attrib["useuri"].lower() == "yes":
                            tfa = (
                                x.attrib["path"],
                                x.attrib["ext"],
                                x.attrib["useuri"],
                                x.attrib["label"],
                                metadata,
                            )
                        else:
                            tfa = (
                                os.path.realpath(x.attrib["path"]),
                                x.attrib["ext"],
                                x.attrib["useuri"],
                                x.attrib["label"],
                                metadata,
                            )
                        track_conf["trackfiles"].append(tfa)

        if is_multi_bigwig:
            metadata = metadata_from_node(x.find("metadata"))

            track_conf["trackfiles"].append(

            # Only pertains to gff3 + blastxml. TODO?
            track_conf["style"] = {t.tag: t.text for t in track.find("options/style")}
        except TypeError:
            track_conf["style"] = {}
            pass
        keys = jc.process_annotations(track_conf)

        if keys:
            for key in keys:
                default_session_data["visibility"][