| Previous changeset 13:1d86925dbb4c (2024-01-22) Next changeset 15:cce8dacb240f (2024-01-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5d84967148d45684d585d4e12b210dc5e12e4776 |
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modified:
abjbrowse2.py jbrowse2.py |
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| diff -r 1d86925dbb4c -r 7c2e28e144f3 abjbrowse2.py --- a/abjbrowse2.py Mon Jan 22 11:52:19 2024 +0000 +++ b/abjbrowse2.py Mon Jan 22 12:05:09 2024 +0000 |
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| b'@@ -15,7 +15,7 @@\n from collections import defaultdict\n \n logging.basicConfig(level=logging.INFO)\n-log = logging.getLogger(\'jbrowse\')\n+log = logging.getLogger("jbrowse")\n TODAY = datetime.datetime.now().strftime("%Y-%m-%d")\n GALAXY_INFRASTRUCTURE_URL = None\n \n@@ -75,20 +75,20 @@\n """\n \n OPACITY_MATH = {\n- \'linear\': """\n+ "linear": """\n var opacity = (score - ({min})) / (({max}) - ({min}));\n """,\n- \'logarithmic\': """\n+ "logarithmic": """\n var opacity = Math.log10(score - ({min})) / Math.log10(({max}) - ({min}));\n """,\n- \'blast\': """\n+ "blast": """\n var opacity = 0;\n if(score == 0.0) {{\n opacity = 1;\n }} else {{\n opacity = (20 - Math.log10(score)) / 180;\n }}\n- """\n+ """,\n }\n \n BREWER_COLOUR_IDX = 0\n@@ -113,15 +113,15 @@\n ]\n \n BREWER_DIVERGING_PALLETES = {\n- \'BrBg\': ("#543005", "#003c30"),\n- \'PiYg\': ("#8e0152", "#276419"),\n- \'PRGn\': ("#40004b", "#00441b"),\n- \'PuOr\': ("#7f3b08", "#2d004b"),\n- \'RdBu\': ("#67001f", "#053061"),\n- \'RdGy\': ("#67001f", "#1a1a1a"),\n- \'RdYlBu\': ("#a50026", "#313695"),\n- \'RdYlGn\': ("#a50026", "#006837"),\n- \'Spectral\': ("#9e0142", "#5e4fa2"),\n+ "BrBg": ("#543005", "#003c30"),\n+ "PiYg": ("#8e0152", "#276419"),\n+ "PRGn": ("#40004b", "#00441b"),\n+ "PuOr": ("#7f3b08", "#2d004b"),\n+ "RdBu": ("#67001f", "#053061"),\n+ "RdGy": ("#67001f", "#1a1a1a"),\n+ "RdYlBu": ("#a50026", "#313695"),\n+ "RdYlGn": ("#a50026", "#006837"),\n+ "Spectral": ("#9e0142", "#5e4fa2"),\n }\n \n def __init__(self):\n@@ -129,15 +129,15 @@\n \n def rgb_from_hex(self, hexstr):\n # http://stackoverflow.com/questions/4296249/how-do-i-convert-a-hex-triplet-to-an-rgb-tuple-and-back\n- return struct.unpack(\'BBB\', binascii.unhexlify(hexstr))\n+ return struct.unpack("BBB", binascii.unhexlify(hexstr))\n \n def min_max_gff(self, gff_file):\n min_val = None\n max_val = None\n- with open(gff_file, \'r\') as handle:\n+ with open(gff_file, "r") as handle:\n for line in handle:\n try:\n- value = float(line.split(\'\\t\')[5])\n+ value = float(line.split("\\t")[5])\n min_val = min(value, (min_val or value))\n max_val = max(value, (max_val or value))\n \n@@ -151,112 +151,128 @@\n return min_val, max_val\n \n def hex_from_rgb(self, r, g, b):\n- return \'#%02x%02x%02x\' % (r, g, b)\n+ return "#%02x%02x%02x" % (r, g, b)\n \n def _get_colours(self):\n- r, g, b = self.BREWER_COLOUR_SCHEMES[self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)]\n+ r, g, b = self.BREWER_COLOUR_SCHEMES[\n+ self.brewer_colour_idx % len(self.BREWER_COLOUR_SCHEMES)\n+ ]\n self.brewer_colour_idx += 1\n return r, g, b\n \n def parse_menus(self, track):\n- trackConfig = {\'menuTemplate\': [{}, {}, {}, {}]}\n+ trackConfig = {"menuTemplate": [{}, {}, {}, {}]}\n \n- if \'menu\' in track[\'menus\']:\n- menu_list = [track[\'menus\'][\'menu\']]\n- if isinstance(track[\'menus\'][\'menu\'], list):\n- menu_list = track[\'menus\'][\'menu\']\n+ if "menu" in track["menus"]:\n+ menu_list = [track["menus"]["menu"]]\n+ if isinstance(track["menus"]["menu"], list):\n+ menu_list = track["menus"]["menu"]\n \n for m in menu_list:\n tpl = {\n- \'action\': m[\'action\'],\n- \'label\': m.get(\'label\', \'{name}\'),\n- \'iconClass\': m.get(\'iconClass\', \'dijitIconBookmark\'),\n+ "action": m["action"],\n+ "label": m.get("label", "{name}"),\n+ "iconClass": m.get("iconClass", "dijitIconBookmark"),\n '..b' x.attrib["label"],\n+ metadata,\n+ )\n+ )\n else:\n # For tracks without files (rest, sparql)\n- track_conf[\'trackfiles\'].append((\n- \'\', # N/A, no path for rest or sparql\n- track.attrib[\'format\'],\n- track.find(\'options/label\').text,\n- {}\n- ))\n+ track_conf["trackfiles"].append(\n+ (\n+ "", # N/A, no path for rest or sparql\n+ track.attrib["format"],\n+ track.find("options/label").text,\n+ {},\n+ )\n+ )\n \n- track_conf[\'category\'] = track.attrib[\'cat\']\n- track_conf[\'format\'] = track.attrib[\'format\']\n- track_conf[\'style\'] = {item.tag: parse_style_conf(item) for item in track.find(\'options/style\')}\n+ track_conf["category"] = track.attrib["cat"]\n+ track_conf["format"] = track.attrib["format"]\n+ track_conf["style"] = {\n+ item.tag: parse_style_conf(item) for item in track.find("options/style")\n+ }\n \n- track_conf[\'style\'] = {item.tag: parse_style_conf(item) for item in track.find(\'options/style\')}\n+ track_conf["style"] = {\n+ item.tag: parse_style_conf(item) for item in track.find("options/style")\n+ }\n \n- track_conf[\'style_labels\'] = {item.tag: parse_style_conf(item) for item in track.find(\'options/style_labels\')}\n+ track_conf["style_labels"] = {\n+ item.tag: parse_style_conf(item)\n+ for item in track.find("options/style_labels")\n+ }\n \n- track_conf[\'conf\'] = etree_to_dict(track.find(\'options\'))\n+ track_conf["conf"] = etree_to_dict(track.find("options"))\n keys = jc.process_annotations(track_conf)\n \n for key in keys:\n- default_session_data[\'visibility\'][track.attrib.get(\'visibility\', \'default_off\')].append(key)\n+ default_session_data["visibility"][\n+ track.attrib.get("visibility", "default_off")\n+ ].append(key)\n \n- default_session_data[\'style\'][key] = track_conf[\'style\'] # TODO do we need this anymore?\n- default_session_data[\'style_labels\'][key] = track_conf[\'style_labels\']\n+ default_session_data["style"][key] = track_conf[\n+ "style"\n+ ] # TODO do we need this anymore?\n+ default_session_data["style_labels"][key] = track_conf["style_labels"]\n \n- default_session_data[\'defaultLocation\'] = root.find(\'metadata/general/defaultLocation\').text\n- default_session_data[\'session_name\'] = root.find(\'metadata/general/session_name\').text\n+ default_session_data["defaultLocation"] = root.find(\n+ "metadata/general/defaultLocation"\n+ ).text\n+ default_session_data["session_name"] = root.find(\n+ "metadata/general/session_name"\n+ ).text\n \n general_data = {\n- \'analytics\': root.find(\'metadata/general/analytics\').text,\n- \'primary_color\': root.find(\'metadata/general/primary_color\').text,\n- \'secondary_color\': root.find(\'metadata/general/secondary_color\').text,\n- \'tertiary_color\': root.find(\'metadata/general/tertiary_color\').text,\n- \'quaternary_color\': root.find(\'metadata/general/quaternary_color\').text,\n- \'font_size\': root.find(\'metadata/general/font_size\').text,\n+ "analytics": root.find("metadata/general/analytics").text,\n+ "primary_color": root.find("metadata/general/primary_color").text,\n+ "secondary_color": root.find("metadata/general/secondary_color").text,\n+ "tertiary_color": root.find("metadata/general/tertiary_color").text,\n+ "quaternary_color": root.find("metadata/general/quaternary_color").text,\n+ "font_size": root.find("metadata/general/font_size").text,\n }\n \n jc.add_default_session(default_session_data)\n jc.add_general_configuration(general_data)\n jc.text_index()\n-\n' |
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| diff -r 1d86925dbb4c -r 7c2e28e144f3 jbrowse2.py --- a/jbrowse2.py Mon Jan 22 11:52:19 2024 +0000 +++ b/jbrowse2.py Mon Jan 22 12:05:09 2024 +0000 |
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| @@ -1188,7 +1188,6 @@ % ddl ) elif self.genome_name is not None: - refName = self.genome_name start = 0 end = 10000 # Booh, hard coded! waiting for https://github.com/GMOD/jbrowse-components/issues/2708 logging.info( |