Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 133:cec274db51c0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 7d28252954cae9f8db5f8a85d8f29cb2865b504b-dirty
author fubar
date Fri, 18 Oct 2024 11:57:55 +0000
parents 1efcc387bef4
children
comparison
equal deleted inserted replaced
132:1efcc387bef4 133:cec274db51c0
444 if logCommands: 444 if logCommands:
445 log.debug(command) 445 log.debug(command)
446 p = subprocess.Popen( 446 p = subprocess.Popen(
447 command, 447 command,
448 cwd=self.outdir, 448 cwd=self.outdir,
449 shell=True, 449 shell=False,
450 stdin=subprocess.PIPE, 450 stdin=subprocess.PIPE,
451 stdout=subprocess.PIPE, 451 stdout=subprocess.PIPE,
452 stderr=subprocess.PIPE, 452 stderr=subprocess.PIPE,
453 ) 453 )
454 output, err = p.communicate() 454 output, err = p.communicate()
552 contig = fl.decode("utf8").strip() 552 contig = fl.decode("utf8").strip()
553 # Merlin 172788 8 60 61 553 # Merlin 172788 8 60 61
554 else: 554 else:
555 faname = gname + ".fa.gz" 555 faname = gname + ".fa.gz"
556 fadest = os.path.realpath(os.path.join(self.outdir, faname)) 556 fadest = os.path.realpath(os.path.join(self.outdir, faname))
557 cmd = "bgzip -i -c %s -I %s.gzi > %s && samtools faidx %s" % ( 557 cmd = ["bgzip", "-i", "-c", fapath, "-I", fadest + ".gzi"]
558 fapath, 558 with open(fadest, "wb") as fout:
559 fadest, 559 self.subprocess_check_call(cmd, output=fout)
560 fadest, 560 cmd = ["samtools", "faidx", fadest]
561 fadest, 561 self.subprocess_check_call(cmd)
562 )
563 self.subprocess_popen(cmd)
564 contig = open(fadest + ".fai", "r").readline().strip() 562 contig = open(fadest + ".fai", "r").readline().strip()
565 adapter = { 563 adapter = {
566 "type": "BgzipFastaAdapter", 564 "type": "BgzipFastaAdapter",
567 "fastaLocation": { 565 "fastaLocation": {
568 "uri": faname, 566 "uri": faname,
955 if useuri: 953 if useuri:
956 url = data 954 url = data
957 else: 955 else:
958 url = tId 956 url = tId
959 dest = os.path.join(self.outdir, url) 957 dest = os.path.join(self.outdir, url)
960 cmd = "bgzip -c %s > %s" % (data, dest) 958 cmd = ["bgzip", "-c", data]
961 self.subprocess_popen(cmd) 959 with open(dest, "wb") as fout:
960 subprocess.run(cmd, stdout=fout)
962 cmd = ["tabix", "-f", "-p", "vcf", dest] 961 cmd = ["tabix", "-f", "-p", "vcf", dest]
963 self.subprocess_check_call(cmd) 962 self.subprocess_check_call(cmd)
964 trackDict = { 963 trackDict = {
965 "type": "VariantTrack", 964 "type": "VariantTrack",
966 "trackId": tId, 965 "trackId": tId,
999 self.trackIdlist.append(tId) 998 self.trackIdlist.append(tId)
1000 999
1001 def _sort_gff(self, data, dest): 1000 def _sort_gff(self, data, dest):
1002 # Only index if not already done 1001 # Only index if not already done
1003 if not os.path.exists(dest): 1002 if not os.path.exists(dest):
1004 cmd = "jbrowse sort-gff '%s' | bgzip -c > '%s'" % ( 1003 e = os.environ
1005 data, 1004 e['SHELL'] = '/bin/sh'
1006 dest, 1005 cmd = ['/bin/sh', '-c', "jbrowse sort-gff %s | bgzip -c > %s" % (data, dest)]
1007 ) 1006 subprocess.run(cmd, env=e)
1008 self.subprocess_popen(cmd)
1009 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest]) 1007 self.subprocess_check_call(["tabix", "-f", "-p", "gff", dest])
1010 1008
1011 def _sort_bed(self, data, dest): 1009 def _sort_bed(self, data, dest):
1012 # Only index if not already done 1010 # Only index if not already done
1013 if not os.path.exists(dest): 1011 if not os.path.exists(dest):
1014 cmd = "sort -k1,1 -k2,2n '%s' | bgzip -c > '%s'" % (data, dest) 1012 cmd = ["sort", "-k1,1", "-k2,2n", data]
1015 self.subprocess_popen(cmd) 1013 ps = subprocess.run(cmd, check=True, capture_output=True)
1014 cmd = ["bgzip", "-c"]
1015 with open(dest, "wb") as fout:
1016 subprocess.run(cmd, input=ps.stdout, stdout=fout)
1016 cmd = ["tabix", "-f", "-p", "bed", dest] 1017 cmd = ["tabix", "-f", "-p", "bed", dest]
1017 self.subprocess_check_call(cmd) 1018 self.subprocess_check_call(cmd)
1018 1019
1019 def add_gff(self, data, trackData): 1020 def add_gff(self, data, trackData):
1020 tId = trackData["label"] 1021 tId = trackData["label"]
1128 ] 1129 ]
1129 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict)) 1130 self.tracksToAdd[trackData["assemblyNames"]].append(copy.copy(trackDict))
1130 self.trackIdlist.append(tId) 1131 self.trackIdlist.append(tId)
1131 1132
1132 def add_paf(self, data, trackData, pafOpts, **kwargs): 1133 def add_paf(self, data, trackData, pafOpts, **kwargs):
1133 canPIF = False 1134 canPIF = True
1134 tname = trackData["name"] 1135 tname = trackData["name"]
1135 tId = trackData["label"] 1136 tId = trackData["label"]
1136 url = tId 1137 url = tId
1137 usePIF = False # much faster if indexed remotely or locally but broken in biocontainer. 1138 usePIF = False # much faster if indexed remotely or locally but broken in biocontainer.
1138 useuri = data.startswith("http://") or data.startswith("https://") 1139 useuri = data.startswith("http://") or data.startswith("https://")
1139 if not useuri: 1140 if not useuri:
1140 if canPIF: 1141 if canPIF:
1141 fakeName = '%s.paf' % tId 1142 fakeName = "%s.paf" % tId
1142 url = "%s.pif.gz" % tId 1143 url = "%s.pif.gz" % tId
1143 cmd = ["cp", data, fakeName] 1144 cmd = ["cp", data, fakeName]
1144 self.subprocess_check_call(cmd) 1145 self.subprocess_check_call(cmd)
1145 cmd = ["jbrowse", "make-pif", fakeName] # jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also 1146 cmd = [
1147 "jbrowse",
1148 "make-pif",
1149 fakeName,
1150 ] # jbrowse pif input.paf --out output.pif.gz # specify output file, creates output.pif.gz.tbi also
1146 self.subprocess_check_call(cmd) 1151 self.subprocess_check_call(cmd)
1147 usePIF = True 1152 usePIF = True
1148 else: 1153 else:
1149 dest = os.path.join(self.outdir, url) 1154 dest = os.path.join(self.outdir, url)
1150 self.symlink_or_copy(os.path.realpath(data), dest) 1155 self.symlink_or_copy(os.path.realpath(data), dest)