Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.py @ 92:3c4db8203fad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f2fba2e6b169256dc9adfa141e3bd59665f08f78
author fubar
date Sun, 21 Apr 2024 04:42:29 +0000
parents 408781c080fc
children 4c517a0041a8
comparison
equal deleted inserted replaced
91:6246925692cb 92:3c4db8203fad
862 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) 862 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
863 self.trackIdlist.append(tId) 863 self.trackIdlist.append(tId)
864 864
865 def add_bam(self, data, trackData, bam_indexes=None, **kwargs): 865 def add_bam(self, data, trackData, bam_indexes=None, **kwargs):
866 tId = trackData["label"] 866 tId = trackData["label"]
867 realFName = trackData["key"] 867 realFName = trackData["path"]
868 useuri = trackData["useuri"].lower() == "yes" 868 useuri = trackData["useuri"].lower() == "yes"
869 categ = trackData["category"] 869 categ = trackData["category"]
870 if useuri: 870 if useuri:
871 url = data 871 url = data
872 else: 872 else:
873 fname = tId 873 fname = tId
874 dest = "%s/%s" % (self.outdir, fname) 874 dest = "%s/%s" % (self.outdir, fname)
875 self.subprocess_check_call(["cp", data, dest])
875 url = fname 876 url = fname
876 bindex = fname + ".bai" 877 bindex = fname + ".bai"
877 self.subprocess_check_call(["cp", data, dest]) 878 bi = bam_indexes.split(",")
878 bi = bam_indexes.split()
879 bam_index = [ 879 bam_index = [
880 x.split(",")[1].strip() 880 x.split(":")[1].strip()
881 for x in bi 881 for x in bi
882 if "," in x and x.split(",")[0].strip() == realFName 882 if ":" in x and x.split(":")[0].strip() == realFName
883 ] 883 ]
884 if len(bam_index) > 0: 884 logging.debug(
885 bam_index = bam_index[0] 885 "===realFName=%s got %s as bam_indexes %s as bi, %s for bam_index"
886 % (realFName, bam_indexes, bi, bam_index)
887 )
888 if len(bam_index) > 0 and os.path.exists(os.path.realpath(bam_index[0])):
889 self.subprocess_check_call(["cp", bam_index[0], bindex])
886 else: 890 else:
887 bam_index = None 891 cmd = ["samtools", "index", "-b", "-o", bindex, data]
888 logging.debug( 892 self.subprocess_check_call(cmd)
889 "===realFName=%s got %s as bi, %s for bam_index"
890 % (realFName, bi, bam_index)
891 )
892 if bam_index is not None and os.path.exists(bam_index):
893 if not os.path.exists(bindex):
894 # bai most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
895 self.subprocess_check_call(["cp", bam_index, bindex])
896 else:
897 # Can happen in exotic condition
898 # e.g. if bam imported as symlink with datatype=unsorted.bam, then datatype changed to bam
899 # => no index generated by galaxy, but there might be one next to the symlink target
900 # this trick allows to skip the bam sorting made by galaxy if already done outside
901 if os.path.exists(os.path.realpath(data) + ".bai"):
902 self.symlink_or_copy(os.path.realpath(data) + ".bai", bindex)
903 else:
904 log.warn("Could not find a bam index (.bai file) for %s", data)
905 trackDict = { 893 trackDict = {
906 "type": "AlignmentsTrack", 894 "type": "AlignmentsTrack",
907 "trackId": tId, 895 "trackId": tId,
908 "name": trackData["name"], 896 "name": trackData["name"],
909 "category": [ 897 "category": [
931 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict) 919 self.tracksToAdd[trackData["assemblyNames"]].append(trackDict)
932 self.trackIdlist.append(tId) 920 self.trackIdlist.append(tId)
933 921
934 def add_cram(self, data, trackData, cram_indexes=None, **kwargs): 922 def add_cram(self, data, trackData, cram_indexes=None, **kwargs):
935 tId = trackData["label"] 923 tId = trackData["label"]
936 realFName = trackData["key"] 924 realFName = trackData["path"]
937 categ = trackData["category"] 925 categ = trackData["category"]
938 useuri = trackData["useuri"].lower() == "yes" 926 useuri = trackData["useuri"].lower() == "yes"
939 gsa = self.assmeta.get(trackData["assemblyNames"], None) 927 gsa = self.assmeta.get(trackData["assemblyNames"], None)
940 if gsa: 928 if gsa:
941 genseqad = gsa[0]["genome_sequence_adapter"] 929 genseqad = gsa[0]["genome_sequence_adapter"]
947 else: 935 else:
948 fname = tId 936 fname = tId
949 dest = os.path.join(self.outdir, fname) 937 dest = os.path.join(self.outdir, fname)
950 url = fname 938 url = fname
951 self.subprocess_check_call(["cp", data, dest]) 939 self.subprocess_check_call(["cp", data, dest])
952 ci = cram_indexes.split() 940 ci = cram_indexes.split(",")
953 cram_index = [ 941 cram_index = [
954 x.split(",")[1].strip() 942 x.split(":")[1].strip()
955 for x in ci 943 for x in ci
956 if "," in x and x.split(",")[0] == realFName 944 if ":" in x and x.split(":")[0].strip() == realFName
957 ] 945 ]
958 if len(cram_index) > 0:
959 cram_index = cram_index[0]
960 else:
961 cram_index = None
962 logging.debug( 946 logging.debug(
963 "=== for %s got %s as cram_indexes, %s for cram_index" 947 "===realFName=%s got %s as cram_indexes %s as ci, %s for cram_index"
964 % (realFName, cram_indexes, cram_index) 948 % (realFName, cram_indexes, ci, cram_index)
965 ) 949 )
966 if cram_index and os.path.exists(cram_index): 950 if len(cram_index) > 0 and os.path.exists(cram_index[0]):
967 if not os.path.exists(dest + ".crai"): 951 if not os.path.exists(dest + ".crai"):
968 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest 952 # most probably made by galaxy and stored in galaxy dirs, need to copy it to dest
969 self.subprocess_check_call( 953 self.subprocess_check_call(
970 ["cp", os.path.realpath(cram_index), dest + ".crai"] 954 ["cp", os.path.realpath(cram_index[0]), dest + ".crai"]
971 ) 955 )
972 else: 956 else:
973 cpath = os.path.realpath(dest) + ".crai" 957 cpath = os.path.realpath(dest) + ".crai"
974 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)] 958 cmd = ["samtools", "index", "-c", "-o", cpath, os.path.realpath(dest)]
975 self.subprocess_check_call(cmd) 959 self.subprocess_check_call(cmd)