Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 79:14ecbe46ae9f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit d03454f949af9f3fff638f6a3e52fe42bc96be3b-dirty
author fubar
date Mon, 01 Apr 2024 09:36:07 +0000
parents 7bb6259ea52f
children dff27c9f6d72
comparison
equal deleted inserted replaced
78:7bb6259ea52f 79:14ecbe46ae9f
401 401
402 class JbrowseConnector(object): 402 class JbrowseConnector(object):
403 def __init__(self, outdir, jbrowse2path): 403 def __init__(self, outdir, jbrowse2path):
404 self.assemblies = [] # these require more than a few line diff. 404 self.assemblies = [] # these require more than a few line diff.
405 self.assmeta = {} 405 self.assmeta = {}
406 self.ass_first_contigs = [] # for default session - these are read as first line of the assembly .fai 406 self.ass_first_contigs = (
407 []
408 ) # for default session - these are read as first line of the assembly .fai
407 self.giURL = GALAXY_INFRASTRUCTURE_URL 409 self.giURL = GALAXY_INFRASTRUCTURE_URL
408 self.outdir = outdir 410 self.outdir = outdir
409 self.jbrowse2path = jbrowse2path 411 self.jbrowse2path = jbrowse2path
410 os.makedirs(self.outdir, exist_ok=True) 412 os.makedirs(self.outdir, exist_ok=True)
411 self.genome_names = [] 413 self.genome_names = []
1400 "displays": [style_data], 1402 "displays": [style_data],
1401 } 1403 }
1402 ) 1404 )
1403 # paf genomes have no tracks associated so nothing for the view 1405 # paf genomes have no tracks associated so nothing for the view
1404 if len(tracks_data) > 0: 1406 if len(tracks_data) > 0:
1405 view_json = {"type": "LinearGenomeView", "tracks": tracks_data} 1407 view_json = {
1406 logging.debug("Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs)) 1408 "type": "LinearGenomeView",
1409 "offsetPx": 0,
1410 "minimized": False,
1411 "tracks": tracks_data,
1412 }
1413 logging.debug(
1414 "Looking for %s in self.ass_ %s" % (gnome, self.ass_first_contigs)
1415 )
1407 first = [x for x in self.ass_first_contigs if x[0] == gnome] 1416 first = [x for x in self.ass_first_contigs if x[0] == gnome]
1408 if len(first) > 0: 1417 if len(first) > 0:
1409 [gnome, refName, end] = first[0] 1418 [gnome, refName, end] = first[0]
1410 start = 1 1419 start = 0
1411 end = int(end) 1420 end = int(end)
1412 refName = self.assmeta[gnome][0].get("genome_firstcontig", None) 1421 refName = self.assmeta[gnome][0].get("genome_firstcontig", None)
1413 drdict = { 1422 drdict = {
1423 "refName": refName,
1424 "start": start,
1425 "end": end,
1414 "reversed": False, 1426 "reversed": False,
1415 "assemblyName": gnome, 1427 "assemblyName": gnome,
1416 "start": start,
1417 "end": end,
1418 "refName": refName,
1419 } 1428 }
1420 else: 1429 else:
1421 ddl = default_data.get("defaultLocation", None) 1430 ddl = default_data.get("defaultLocation", None)
1422 if ddl: 1431 if ddl:
1423 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl) 1432 loc_match = re.search(r"^([^:]+):([\d,]*)\.*([\d,]*)$", ddl)
1424 # allow commas like 100,000 but ignore as integer 1433 # allow commas like 100,000 but ignore as integer
1425 if loc_match: 1434 if loc_match:
1426 refName = loc_match.group(1) 1435 refName = loc_match.group(1)
1427 drdict["refName"] = refName 1436 drdict["refName"] = refName
1428 if loc_match.group(2) > "": 1437 if loc_match.group(2) > "":
1429 drdict["start"] = int(loc_match.group(2).replace(",", "")) 1438 drdict["start"] = int(
1439 loc_match.group(2).replace(",", "")
1440 )
1430 if loc_match.group(3) > "": 1441 if loc_match.group(3) > "":
1431 drdict["end"] = int(loc_match.group(3).replace(",", "")) 1442 drdict["end"] = int(loc_match.group(3).replace(",", ""))
1432 else: 1443 else:
1433 logging.info( 1444 logging.info(
1434 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix" 1445 "@@@ regexp could not match contig:start..end in the supplied location %s - please fix"
1461 with open(self.config_json_file, "w") as config_file: 1472 with open(self.config_json_file, "w") as config_file:
1462 json.dump(self.config_json, config_file, indent=2) 1473 json.dump(self.config_json, config_file, indent=2)
1463 1474
1464 def add_defsess_to_index(self, data): 1475 def add_defsess_to_index(self, data):
1465 """ 1476 """
1466 Broken in Anthony's PR because only ever dealt with the first assembly. 1477 This was included on request of the new codeowner from Anthony's IUC PR.
1467 1478 Now fixed to deal with each assembly and tracks separately.
1479 Originally used only the first assembly, putting all tracks there and
1480 generally falling apart when tested with 2 or more. Seems ironic that
1481 this vital feature was never tested given the rejection of my original IUC PR
1482 because it was not there. And no, reviewer, I do not want this important piece of history
1483 removed. I prefer that it remain here since it has caused me considerable discomfort.
1484
1485 ----------------------------------------------------------
1468 Add some default session settings: set some assemblies/tracks on/off 1486 Add some default session settings: set some assemblies/tracks on/off
1469 1487
1470 This allows to select a default view: 1488 This allows to select a default view:
1471 - jb type (Linear, Circular, etc) 1489 - jb type (Linear, Circular, etc)
1472 - default location on an assembly 1490 - default location on an assembly
1746 assconf = jc.config_json.get("assemblies", []) 1764 assconf = jc.config_json.get("assemblies", [])
1747 assconf += jc.assemblies 1765 assconf += jc.assemblies
1748 jc.config_json["assemblies"] = assconf 1766 jc.config_json["assemblies"] = assconf
1749 logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names)) 1767 logging.debug("assemblies=%s, gnames=%s" % (assconf, jc.genome_names))
1750 jc.write_config() 1768 jc.write_config()
1751 jc.add_default_session(default_session_data) 1769 # jc.add_default_session(default_session_data)
1770 # note that this can be left in the config.json but has NO EFFECT if add_defsess_to_index is called.
1752 jc.add_defsess_to_index(default_session_data) 1771 jc.add_defsess_to_index(default_session_data)
1753 # jc.text_index() not sure what broke here. 1772 # jc.text_index() not sure what broke here.