jbrowse2: jbrowse2.py comparison

comparison jbrowse2.py @ 93:4c517a0041a8 draft

planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4

author	fubar
date	Wed, 24 Apr 2024 02:29:32 +0000
parents	3c4db8203fad
children	74074746ccd8

comparison

equal deleted inserted replaced

-:3c4db8203fad
+:4c517a0041a8
 from collections import defaultdict
 logging.basicConfig(level=logging.DEBUG)
 log = logging.getLogger("jbrowse")
-JB2VER = "v2.10.3"
+JB2VER = "v2.11.0"
 # version pinned if cloning - but not cloning now
 logCommands = True
 # useful for seeing what's being written but not for production setups
 TODAY = datetime.datetime.now().strftime("%Y-%m-%d")
 SELF_LOCATION = os.path.dirname(os.path.realpath(__file__))
 if genome_name == primaryGenome:  # first one
 this_genome["genome_name"] = genome_name  # first one for all tracks
 this_genome["genome_sequence_adapter"] = assem["sequence"][
 "adapter"
 ]
-this_genome["genome_firstcontig"] = None
+this_genome["genome_firstcontig"] = first_contig
-if not useuri:
-fl = open(fapath, "r").readline()
-fls = fl.strip().split(">")
-if len(fls) > 1:
-fl = fls[1]
-if len(fl.split()) > 1:
-this_genome["genome_firstcontig"] = fl.split()[
-0
-].strip()
-else:
-this_genome["genome_firstcontig"] = fl
-else:
-try:
-scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
-scontext.verify_mode = ssl.VerifyMode.CERT_NONE
-with urllib.request.urlopen(
-url=fapath + ".fai", context=scontext
-) as f:
-fl = f.readline()
-except Exception:
-fl = None
-if fl:  # is first row of the text fai so the first contig name
-this_genome["genome_firstcontig"] = (
-fl.decode("utf8").strip().split()[0]
-)
 assmeta.append(this_genome)
 self.assemblies += assembly
 self.assmeta[primaryGenome] = assmeta
 self.tracksToAdd[primaryGenome] = []
 return primaryGenome
 """added code to grab the first contig name and length for broken default session from Anthony and Helena's code
 that poor Bjoern is trying to figure out.
 """
 if useuri:
 faname = fapath
-adapter = {
-"type": "BgzipFastaAdapter",
-"fastaLocation": {"uri": faname, "locationType": "UriLocation"},
-"faiLocation": {"uri": faname + ".fai", "locationType": "UriLocation"},
-"gziLocation": {"uri": faname + ".gzi", "locationType": "UriLocation"},
-}
 scontext = ssl.SSLContext(ssl.PROTOCOL_TLS)
 scontext.verify_mode = ssl.VerifyMode.CERT_NONE
 with urllib.request.urlopen(url=faname + ".fai", context=scontext) as f:
 fl = f.readline()
 contig = fl.decode("utf8").strip()
 fadest,
 fadest,
 fadest,
 )
 self.subprocess_popen(cmd)
-adapter = {
-"type": "BgzipFastaAdapter",
-"fastaLocation": {
-"uri": faname,
-},
-"faiLocation": {
-"uri": faname + ".fai",
-},
-"gziLocation": {
-"uri": faname + ".gzi",
-},
-}
 contig = open(fadest + ".fai", "r").readline().strip()
+adapter = {
+"type": "BgzipFastaAdapter",
+"fastaLocation": {
+"uri": faname,
+},
+"faiLocation": {
+"uri": faname + ".fai",
+},
+"gziLocation": {
+"uri": faname + ".gzi",
+},
+}
 first_contig = contig.split()[:2]
 first_contig.insert(0, gname)
 trackDict = {
 "name": gname,
 "sequence": {
 self.subprocess_check_call(["cp", data, dest])
 url = fname
 bindex = fname + ".bai"
 bi = bam_indexes.split(",")
 bam_index = [
-x.split(":")[1].strip()
+x.split(" ~ ")[1].strip()
 for x in bi
-if ":" in x and x.split(":")[0].strip() == realFName
+if " ~ " in x and x.split(" ~ ")[0].strip() == realFName
 ]
 logging.debug(
 "===realFName=%s got %s as bam_indexes %s as bi, %s for bam_index"
 % (realFName, bam_indexes, bi, bam_index)
 )
 dest = os.path.join(self.outdir, fname)
 url = fname
 self.subprocess_check_call(["cp", data, dest])
 ci = cram_indexes.split(",")
 cram_index = [
-x.split(":")[1].strip()
+x.split(" ~ ")[1].strip()
 for x in ci
-if ":" in x and x.split(":")[0].strip() == realFName
+if " ~ " in x and x.split(" ~ ")[0].strip() == realFName
 ]
 logging.debug(
 "===realFName=%s got %s as cram_indexes %s as ci, %s for cram_index"
 % (realFName, cram_indexes, ci, cram_index)
 )
 url = data
 nrow = self.getNrow(url)
 categ = trackData["category"]
 pg = pafOpts["genome"].split(",")
 pgc = [x.strip() for x in pg if x.strip() > ""]
-gnomes = [x.split(":") for x in pgc]
+gnomes = [x.split(" ~ ") for x in pgc]
+logging.debug("pg=%s, gnomes=%s" % (pg, gnomes))
 passnames = [trackData["assemblyNames"]]  # always first
 for i, (gpath, gname) in enumerate(gnomes):
 # may have been forgotten by user for uri
 if len(gname) == 0:
 gn = os.path.basename(gpath)
 # trouble from spacey names in command lines avoidance
 if len(gname.split()) > 1:
 gname = gname.split()[0]
 if gname not in passnames:
 passnames.append(gname)
-useuri = gpath.startswith("http://") or gpath.startswith("https://")
+useuri = pafOpts["useuri"] == "true"
 if gname not in self.genome_names:
 # ignore if already there - eg for duplicates among pafs.
 asstrack, first_contig = self.make_assembly(gpath, gname, useuri)
 self.genome_names.append(gname)
 self.tracksToAdd[gname] = []
 trackI = 0
 for ass in root.findall("assembly"):
 genomes = [
 {
 "path": x.attrib["path"],
-"label": x.attrib["label"],
+"label": x.attrib["label"].split(" ")[0].replace(",", ""),
 "useuri": x.attrib["useuri"],
 "meta": metadata_from_node(x.find("metadata")),
 }
 for x in ass.findall("metadata/genomes/genome")
 ]
 pass
 trackfiles = track.findall("files/trackFile")
 if trackfiles:
 for x in trackfiles:
-track_conf["label"] = "%s_%d" % (x.attrib["label"], trackI)
+track_conf["label"] = "%s_%d" % (
+x.attrib["label"].replace(" ", "_").replace(",", ""),
+trackI,
+)
 trackI += 1
 track_conf["useuri"] = x.attrib["useuri"]
 if is_multi_bigwig:
 multi_bigwig_paths.append(
 (

Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 93:4c517a0041a8 draft