Mercurial > repos > artbio > lumpy_sv

comparison extractSplitReads_BwaMem.py @ 6:48e97429a749 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit 37c0f0938a5cad74c954a89827a6a08bbbb81cb0
author artbio
date Mon, 08 Jul 2024 22:23:10 +0000
parents 1ed8619a5611
children
comparison
equal deleted inserted replaced
5:6ae3a402b9af 6:48e97429a749
19 sam = SAM(samList) 19 sam = SAM(samList)
20 if includeDups == 0 and (1024 & sam.flag) == 1024: 20 if includeDups == 0 and (1024 & sam.flag) == 1024:
21 continue 21 continue
22 for el in sam.tags: 22 for el in sam.tags:
23 if "SA:" in el: 23 if "SA:" in el:
24 if(len(el.split(";"))) <= numSplits: 24 if (len(el.split(";"))) <= numSplits:
25 split = 1 25 split = 1
26 mate = el.split(",") 26 mate = el.split(",")
27 mateCigar = mate[3] 27 mateCigar = mate[3]
28 mateFlag = int(0) 28 mateFlag = int(0)
29 if mate[2] == "-": 29 if mate[2] == "-":
101 elif (flag & 0x0010): 101 elif (flag & 0x0010):
102 cigarOpStrings = cigarSearch.findall(cigar) 102 cigarOpStrings = cigarSearch.findall(cigar)
103 cigarOps = [] 103 cigarOps = []
104 for opString in cigarOpStrings: 104 for opString in cigarOpStrings:
105 cigarOpList = atomicCigarSearch.findall(opString) 105 cigarOpList = atomicCigarSearch.findall(opString)
106 # print cigarOpList
107 # "struct" for the op and it's length 106 # "struct" for the op and it's length
108 cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1]) 107 cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
109 # add to the list of cigarOps 108 # add to the list of cigarOps
110 cigarOps.append(cigar) 109 cigarOps.append(cigar)
111 cigarOps = cigarOps 110 cigarOps = cigarOps
118 cigarOpList = atomicCigarSearch.findall(opString) 117 cigarOpList = atomicCigarSearch.findall(opString)
119 # "struct" for the op and it's length 118 # "struct" for the op and it's length
120 cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1]) 119 cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
121 # add to the list of cigarOps 120 # add to the list of cigarOps
122 cigarOps.append(cigar) 121 cigarOps.append(cigar)
123 # cigarOps = cigarOps 122 return cigarOps
124 return(cigarOps)
125 123
126 124
127 def calcQueryPosFromCigar(cigarOps): 125 def calcQueryPosFromCigar(cigarOps):
128 qsPos = 0 126 qsPos = 0
129 qePos = 0 127 qePos = 0
200 parser.add_option("-d", "--includeDups", dest="includeDups", 198 parser.add_option("-d", "--includeDups", dest="includeDups",
201 action="store_true", default=0, 199 action="store_true", default=0,
202 help='''Include alignments marked as duplicates. 200 help='''Include alignments marked as duplicates.
203 Default=False''') 201 Default=False''')
204 parser.add_option("-m", "--minNonOverlap", dest="minNonOverlap", 202 parser.add_option("-m", "--minNonOverlap", dest="minNonOverlap",
205 default=20, type="int", help='''minimum non-overlap between 203 default=20, type="int",
204 help='''minimum non-overlap between
206 split alignments on the query (default=20)''', 205 split alignments on the query (default=20)''',
207 metavar="INT") 206 metavar="INT")
208 (opts, args) = parser.parse_args() 207 (opts, args) = parser.parse_args()
209 if opts.inFile is None: 208 if opts.inFile is None:
210 parser.print_help() 209 parser.print_help()