comparison jbrowse2.py @ 65:c81902830900 draft

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

64:497fd2d27aa2

import tempfile
import urllib.request
import xml.etree.ElementTree as ET
from collections import defaultdict

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

JB2VER = "v2.10.3"
# version pinned for cloning

                        "displays": [style_data],
                    }
                )
            # The view for the assembly we're adding
            view_json = {"type": "LinearGenomeView", "tracks": tracks_data}
            refName = None
            drdict = {
                "reversed": False,
                "assemblyName": gnome,
                "start": 1,
                "end": 100000,
                "refName": "x",
            }

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

                else:
                    logging.info(
                        "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
                        % ddl
                    )
            else:
                drdict["refName"] = gnome
            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,
                ]

65:c81902830900

import tempfile
import urllib.request
import xml.etree.ElementTree as ET
from collections import defaultdict

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

JB2VER = "v2.10.3"
# version pinned for cloning

                        "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

                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,
                ]