Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 71:e26a8a6d2d2e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cf208cecf0140ff43d145a44713ab7108057fb8b
author fubar
date Sat, 30 Mar 2024 07:15:04 +0000
parents 5f0ee87daef4
children 2bdb748df098
comparison
equal deleted inserted replaced
70:5f0ee87daef4 71:e26a8a6d2d2e
376 def __init__(self, outdir, jbrowse2path): 376 def __init__(self, outdir, jbrowse2path):
377 self.assemblies = [] # these require more than a few line diff. 377 self.assemblies = [] # these require more than a few line diff.
378 self.assmeta = {} 378 self.assmeta = {}
379 self.giURL = GALAXY_INFRASTRUCTURE_URL 379 self.giURL = GALAXY_INFRASTRUCTURE_URL
380 self.outdir = outdir 380 self.outdir = outdir
381 self.genome_firstcontig = None
382 self.jbrowse2path = jbrowse2path 381 self.jbrowse2path = jbrowse2path
383 os.makedirs(self.outdir, exist_ok=True) 382 os.makedirs(self.outdir, exist_ok=True)
384 self.genome_names = [] 383 self.genome_names = []
385 self.trackIdlist = [] 384 self.trackIdlist = []
386 self.tracksToAdd = {} 385 self.tracksToAdd = {}
1123 lab = trackData["label"] 1122 lab = trackData["label"]
1124 if len(gname.split()) > 1: 1123 if len(gname.split()) > 1:
1125 gname = gname.split()[0] 1124 gname = gname.split()[0]
1126 passnames.append(gname) 1125 passnames.append(gname)
1127 # trouble from spacey names in command lines avoidance 1126 # trouble from spacey names in command lines avoidance
1127 useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
1128 "https://"
1129 )
1130 if not useuri:
1131 url = "%s.paf" % (lab)
1132 else:
1133 url = data
1128 if gname not in self.genome_names: 1134 if gname not in self.genome_names:
1129 # ignore if already there - eg for duplicates among pafs. 1135 # ignore if already there - eg for duplicates among pafs.
1130 useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(
1131 "https://"
1132 )
1133 asstrack = self.make_assembly(pgpaths[i], gname, useuri) 1136 asstrack = self.make_assembly(pgpaths[i], gname, useuri)
1134 self.genome_names.append(gname) 1137 self.genome_names.append(gname)
1135 self.tracksToAdd[gname] = [] 1138 self.tracksToAdd[gname] = []
1136 self.assemblies.append(asstrack) 1139 self.assemblies.append(asstrack)
1137 if not useuri: 1140 if not useuri:
1138 url = "%s.paf" % (lab)
1139 dest = "%s/%s" % (self.outdir, url) 1141 dest = "%s/%s" % (self.outdir, url)
1140 self.symlink_or_copy(os.path.realpath(data), dest) 1142 self.symlink_or_copy(os.path.realpath(data), dest)
1141 else:
1142 url = data
1143 trackDict = { 1143 trackDict = {
1144 "type": "SyntenyTrack", 1144 "type": "SyntenyTrack",
1145 "trackId": tId, 1145 "trackId": tId,
1146 "assemblyNames": passnames, 1146 "assemblyNames": passnames,
1147 "category": [ 1147 "category": [
1580 item.tag: parse_style_conf(item) 1580 item.tag: parse_style_conf(item)
1581 for item in track.find("options/style") 1581 for item in track.find("options/style")
1582 } 1582 }
1583 else: 1583 else:
1584 default_session_data["style"][key] = {} 1584 default_session_data["style"][key] = {}
1585 logging.warn("@@@@ no options/style found for %s" % (key)) 1585 logging.debug("@@@@ no options/style found for %s" % (key))
1586 1586
1587 if track.find("options/style_labels"): 1587 if track.find("options/style_labels"):
1588 default_session_data["style_labels"][key] = { 1588 default_session_data["style_labels"][key] = {
1589 item.tag: parse_style_conf(item) 1589 item.tag: parse_style_conf(item)
1590 for item in track.find("options/style_labels") 1590 for item in track.find("options/style_labels")
1605 "quaternary_color": root.find("metadata/general/quaternary_color").text, 1605 "quaternary_color": root.find("metadata/general/quaternary_color").text,
1606 "font_size": root.find("metadata/general/font_size").text, 1606 "font_size": root.find("metadata/general/font_size").text,
1607 } 1607 }
1608 jc.add_general_configuration(general_data) 1608 jc.add_general_configuration(general_data)
1609 trackconf = jc.config_json.get("tracks", []) 1609 trackconf = jc.config_json.get("tracks", [])
1610 logging.warn("++++++++++++ genome_names=%s" % jc.genome_names)
1611 for gnome in jc.genome_names: 1610 for gnome in jc.genome_names:
1612 trackconf += jc.tracksToAdd[gnome] 1611 trackconf += jc.tracksToAdd[gnome]
1613 jc.config_json["tracks"] = trackconf 1612 jc.config_json["tracks"] = trackconf
1614 assconf = jc.config_json.get("assemblies", []) 1613 assconf = jc.config_json.get("assemblies", [])
1615 assconf += jc.assemblies 1614 assconf += jc.assemblies
1616 jc.config_json["assemblies"] = assconf 1615 jc.config_json["assemblies"] = assconf
1617 logging.warn("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) 1616 logging.debug("&&&assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
1618 jc.write_config() 1617 jc.write_config()
1619 jc.add_default_session(default_session_data) 1618 jc.add_default_session(default_session_data)
1620 # jc.text_index() not sure what broke here. 1619 # jc.text_index() not sure what broke here.