Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 128:fce4ed3b1702 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a46026a5ea4f075b9053448616f22e8a83fa699a
author bgruening
date Mon, 07 Oct 2024 06:30:43 +0000
parents fbabf7498471
children e188a9d25ed2
comparison
equal deleted inserted replaced
127:fbabf7498471 128:fce4ed3b1702
1134 tId = trackData["label"] 1134 tId = trackData["label"]
1135 url = tId 1135 url = tId
1136 usePIF = False # much faster if indexed remotely or locally 1136 usePIF = False # much faster if indexed remotely or locally
1137 useuri = data.startswith("http://") or data.startswith("https://") 1137 useuri = data.startswith("http://") or data.startswith("https://")
1138 if not useuri: 1138 if not useuri:
1139 dest = os.path.join(self.outdir, url) 1139 # self.symlink_or_copy(os.path.realpath(data), url)
1140 self.symlink_or_copy(os.path.realpath(data), dest) 1140 # cmd = ["jbrowse", "make-pif", url]
1141 cmd = ["jbrowse", "make-pif", dest] 1141 url = '%s.pif.gz' % tId
1142 cmd = "sort -b -n -k1,1 -k2,3 -k3,4 '%s' | bgzip -c > '%s'" % (data, url)
1143 self.subprocess_popen(cmd)
1144 cmd = ["tabix", "-b", "3", "-e", "4", "-f", url]
1142 self.subprocess_check_call(cmd) 1145 self.subprocess_check_call(cmd)
1143 usePIF = True 1146 usePIF = True
1144 url = '%s.pif.gz' % tId 1147 nrow = 1
1145 nrow = self.getNrow(dest)
1146 else: 1148 else:
1147 url = data 1149 url = data
1148 if data.endswith(".pif.gz") or data.endswith(".paf.gz"): # is tabix 1150 if data.endswith(".pif.gz") or data.endswith(".paf.gz"): # is tabix
1149 usePIF = True 1151 usePIF = True
1150 nrow = 1 1152 nrow = 1
1729 trakdat = jc.tracksToAdd[primaryGenome] 1731 trakdat = jc.tracksToAdd[primaryGenome]
1730 stile = {} 1732 stile = {}
1731 for trak in trakdat: 1733 for trak in trakdat:
1732 if trak["trackId"] == key: 1734 if trak["trackId"] == key:
1733 stile = trak.get("style", {}) 1735 stile = trak.get("style", {})
1734 if track.find("options/style"): 1736 if len(track.find("options/style")) > 0:
1735 for item in track.find("options/style"): 1737 for item in track.find("options/style"):
1736 if item.text: 1738 if item.text:
1737 stile[item.tag] = parse_style_conf(item) 1739 stile[item.tag] = parse_style_conf(item)
1738 logging.debug("stile=%s" % stile) 1740 logging.debug("stile=%s" % stile)
1739 default_session_data[primaryGenome]["style"][key] = stile 1741 default_session_data[primaryGenome]["style"][key] = stile