comparison autogenJB2.py @ 67:cefe9dbf1d80 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 6dac6d6debf44c68eae2785e926fb8420f76958e-dirty

66:bc10ad1dfb98

import os
import sys

from jbrowse2 import JbrowseConnector as jbC

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


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
    parser.add_argument(

                    guseuri.append("no")
            jc = jbC(
                outdir=args.outdir,
                jbrowse2path=args.jbrowse2path,
            )
            genomes=[
                    {
                        "path": x,
                        "label": genome_names[i],
                        "useuri": guseuri[i],
                        "meta": {

                            "dataset_dname": genome_names[i],
                        },
                    }
                    for i, x in enumerate(genome_paths)
                ],
            logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
            assref_name = jc.process_genomes(genomes[0])
            default_session_data = {
                "visibility": {
                    "default_on": [],

            listtracks = trackList
            # foo.paf must have a foo_paf.fasta or fasta.gz to match
            tnames = [x[2] for x in listtracks]
            texts = [x[1] for x in listtracks]
            for i, track in enumerate(listtracks):
                track_conf = {"trackfiles": [], "category": "autogenerated", "assemblyNames": assref_name}
                tpath, trext, trackname = track[:3]
                track_conf["dataset_id"] = trackname
                useuri = "no"
                if tpath.startswith("http://") or tpath.startswith("https://"):
                    useuri = "yes"

                if keys:
                    for key in keys:
                        if trext in [
                            "bigwig",
                            "gff", "gff3",
                            "vcf",
                            "maf",
                        ]:
                            default_session_data["visibility"]["default_on"].append(key)
                        else:

                        if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
                            ttype = "LinearBasicDisplay"
                            if trext == "vcf":
                                ttype = "LinearVariantDisplay"
                            style_json = {
                            "type": ttype,
                            "trackShowLabels": False,
                            "trackShowDescriptions": False
                            }
                            default_session_data["style"][key] = style_json
            # general_data = {
            # "analytics": root.find("metadata/general/analytics").text,
            # "primary_color": root.find("metadata/general/primary_color").text,

            # }
            jc.add_general_configuration({})
            trackconf = jc.config_json.get("tracks", [])
            for gnome in jc.genome_names:
                trackconf += jc.tracksToAdd[gnome]
            jc.config_json["tracks"] = trackconf
            jc.write_config()
            default_session_data.update(
                {"session_name": sessName}
            )
            track_conf.update(default_session_data)
            jc.add_default_session(default_session_data)
            # jc.text_index() not sure what broke here.
    else:
        sys.stderr.write(
            "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
        )

67:cefe9dbf1d80

import os
import sys

from jbrowse2 import JbrowseConnector as jbC


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

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="", epilog="")
    parser.add_argument("--sessName", help="Session name", default="AutoJBrowse")
    parser.add_argument(

                    guseuri.append("no")
            jc = jbC(
                outdir=args.outdir,
                jbrowse2path=args.jbrowse2path,
            )
            genomes = (
                [
                    {
                        "path": x,
                        "label": genome_names[i],
                        "useuri": guseuri[i],
                        "meta": {

                            "dataset_dname": genome_names[i],
                        },
                    }
                    for i, x in enumerate(genome_paths)
                ],
            )
            logging.warn("#!!! paths=%s, genomes=%s" % (genome_paths, genomes))
            assref_name = jc.process_genomes(genomes[0])
            default_session_data = {
                "visibility": {
                    "default_on": [],

            listtracks = trackList
            # foo.paf must have a foo_paf.fasta or fasta.gz to match
            tnames = [x[2] for x in listtracks]
            texts = [x[1] for x in listtracks]
            for i, track in enumerate(listtracks):
                track_conf = {
                    "trackfiles": [],
                    "category": "autogenerated",
                    "assemblyNames": assref_name,
                }
                tpath, trext, trackname = track[:3]
                track_conf["dataset_id"] = trackname
                useuri = "no"
                if tpath.startswith("http://") or tpath.startswith("https://"):
                    useuri = "yes"

                if keys:
                    for key in keys:
                        if trext in [
                            "bigwig",
                            "gff",
                            "gff3",
                            "vcf",
                            "maf",
                        ]:
                            default_session_data["visibility"]["default_on"].append(key)
                        else:

                        if trext in ["gff", "gff3", "bed", "vcf", "maf", "blastxml"]:
                            ttype = "LinearBasicDisplay"
                            if trext == "vcf":
                                ttype = "LinearVariantDisplay"
                            style_json = {
                                "type": ttype,
                                "trackShowLabels": False,
                                "trackShowDescriptions": False,
                            }
                            default_session_data["style"][key] = style_json
            # general_data = {
            # "analytics": root.find("metadata/general/analytics").text,
            # "primary_color": root.find("metadata/general/primary_color").text,

            # }
            jc.add_general_configuration({})
            trackconf = jc.config_json.get("tracks", [])
            for gnome in jc.genome_names:
                trackconf += jc.tracksToAdd[gnome]
            logging.warn(
                "^^%% adding trackconf=%s for gnome %s" % (trackconf, gnome)
            )
            jc.config_json["tracks"] = trackconf
            jc.write_config()
            default_session_data.update({"session_name": sessName})
            track_conf.update(default_session_data)
            jc.add_default_session(default_session_data)
            # jc.text_index() not sure what broke here.
    else:
        sys.stderr.write(
            "!!!! Collection has no suitable trackfiles for autogenJB2 - nothing to process"
        )