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annotate extractSplitReads_BwaMem.py @ 12:b3fb23bbca8e draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit 03ac2f3182f9e72db31297fa9e2fd5f0802343ea
author drosofff
date Sun, 18 Dec 2016 10:35:43 -0500
parents 8b3daa745d9b
children
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8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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1 #!/usr/bin/env python
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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2
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3 import sys
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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4 import getopt
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5 import string
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6 from optparse import OptionParser
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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7 import re
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8
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9 def extractSplitsFromBwaMem(inFile,numSplits,includeDups,minNonOverlap):
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10 if inFile == "stdin":
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11 data = sys.stdin
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12 else:
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13 data = open(inFile, 'r')
8b3daa745d9b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy commit c0bfc4b2215705e1b5fd1d4e60b1d72e5da13c92
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14 for line in data:
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15 split = 0
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16 if line[0] == '@':
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17 print line.strip()
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18 continue
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19 samList = line.strip().split('\t')
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20 sam = SAM(samList)
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21 if includeDups==0 and (1024 & sam.flag)==1024:
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22 continue
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23 for el in sam.tags:
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24 if "SA:" in el:
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25 if(len(el.split(";")))<=numSplits:
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26 split = 1
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27 mate = el.split(",")
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28 mateCigar = mate[3]
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29 mateFlag = int(0)
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30 if mate[2]=="-": mateFlag = int(16)
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31 if split:
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32 read1 = sam.flag & 64
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33 if read1 == 64: tag = "_1"
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34 else: tag="_2"
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35 samList[0] = sam.query + tag
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36 readCigar = sam.cigar
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37 readCigarOps = extractCigarOps(readCigar,sam.flag)
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38 readQueryPos = calcQueryPosFromCigar(readCigarOps)
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39 mateCigarOps = extractCigarOps(mateCigar,mateFlag)
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40 mateQueryPos = calcQueryPosFromCigar(mateCigarOps)
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41 overlap = calcQueryOverlap(readQueryPos.qsPos,readQueryPos.qePos,mateQueryPos.qsPos,mateQueryPos.qePos)
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42 nonOverlap1 = 1 + readQueryPos.qePos - readQueryPos.qsPos - overlap
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43 nonOverlap2 = 1 + mateQueryPos.qePos - mateQueryPos.qsPos - overlap
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44 mno = min(nonOverlap1, nonOverlap2)
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45 if mno >= minNonOverlap:
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46 print "\t".join(samList)
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47
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48 #--------------------------------------------------------------------------------------------------
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49 # functions
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50 #--------------------------------------------------------------------------------------------------
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51
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52 class SAM (object):
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53 """
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54 __very__ basic class for SAM input.
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55 """
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56 def __init__(self, samList = []):
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57 if len(samList) > 0:
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58 self.query = samList[0]
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59 self.flag = int(samList[1])
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60 self.ref = samList[2]
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61 self.pos = int(samList[3])
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62 self.mapq = int(samList[4])
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63 self.cigar = samList[5]
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64 self.matRef = samList[6]
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65 self.matePos = int(samList[7])
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66 self.iSize = int(samList[8])
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67 self.seq = samList[9]
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68 self.qual = samList[10]
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69 self.tags = samList[11:]#tags is a list of each tag:vtype:value sets
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70 self.valid = 1
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71 else:
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72 self.valid = 0
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73 self.query = 'null'
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74
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75 def extractTagValue (self, tagID):
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76 for tag in self.tags:
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77 tagParts = tag.split(':', 2);
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78 if (tagParts[0] == tagID):
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79 if (tagParts[1] == 'i'):
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80 return int(tagParts[2]);
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81 elif (tagParts[1] == 'H'):
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82 return int(tagParts[2],16);
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83 return tagParts[2];
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84 return None;
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85
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86 #-----------------------------------------------
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87 cigarPattern = '([0-9]+[MIDNSHP])'
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88 cigarSearch = re.compile(cigarPattern)
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89 atomicCigarPattern = '([0-9]+)([MIDNSHP])'
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90 atomicCigarSearch = re.compile(atomicCigarPattern)
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91
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92 def extractCigarOps(cigar,flag):
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93 if (cigar == "*"):
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94 cigarOps = []
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95 elif (flag & 0x0010):
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96 cigarOpStrings = cigarSearch.findall(cigar)
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97 cigarOps = []
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98 for opString in cigarOpStrings:
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99 cigarOpList = atomicCigarSearch.findall(opString)
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100 # print cigarOpList
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101 # "struct" for the op and it's length
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102 cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
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103 # add to the list of cigarOps
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104 cigarOps.append(cigar)
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105 cigarOps = cigarOps
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106 cigarOps.reverse()
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107 ##do in reverse order because negative strand##
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108 else:
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109 cigarOpStrings = cigarSearch.findall(cigar)
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110 cigarOps = []
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111 for opString in cigarOpStrings:
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112 cigarOpList = atomicCigarSearch.findall(opString)
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113 # "struct" for the op and it's length
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114 cigar = cigarOp(cigarOpList[0][0], cigarOpList[0][1])
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115 # add to the list of cigarOps
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116 cigarOps.append(cigar)
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117 # cigarOps = cigarOps
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118 return(cigarOps)
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119
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120 def calcQueryPosFromCigar(cigarOps):
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121 qsPos = 0
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122 qePos = 0
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123 qLen = 0
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124 # if first op is a H, need to shift start position
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125 # the opPosition counter sees if the for loop is looking at the first index of the cigar object
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126 opPosition = 0
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127 for cigar in cigarOps:
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128 if opPosition == 0 and (cigar.op == 'H' or cigar.op == 'S'):
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129 qsPos += cigar.length
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130 qePos += cigar.length
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131 qLen += cigar.length
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132 elif opPosition > 0 and (cigar.op == 'H' or cigar.op == 'S'):
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133 qLen += cigar.length
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134 elif cigar.op == 'M' or cigar.op == 'I':
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135 qePos += cigar.length
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136 qLen += cigar.length
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137 opPosition += 1
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138 d = queryPos(qsPos, qePos, qLen);
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139 return d
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140
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141 class cigarOp (object):
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142 """
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143 sturct to store a discrete CIGAR operations
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144 """
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145 def __init__(self, opLength, op):
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146 self.length = int(opLength)
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147 self.op = op
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148
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149 class queryPos (object):
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150 """
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151 struct to store the start and end positions of query CIGAR operations
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152 """
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153 def __init__(self, qsPos, qePos, qLen):
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154 self.qsPos = int(qsPos)
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155 self.qePos = int(qePos)
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156 self.qLen = int(qLen)
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157
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158
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159 def calcQueryOverlap(s1,e1,s2,e2):
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160 o = 1 + min(e1, e2) - max(s1, s2)
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161 return max(0, o)
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162
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163 ###############################################
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164
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165 class Usage(Exception):
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166 def __init__(self, msg):
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167 self.msg = msg
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168
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169 def main():
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170
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171 usage = """%prog -i <file>
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172
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173 extractSplitReads_BwaMem v0.1.0
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174 Author: Ira Hall
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175 Description: Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates.
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176 Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405.
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177 """
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178 parser = OptionParser(usage)
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179
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180 parser.add_option("-i", "--inFile", dest="inFile",
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181 help="A SAM file or standard input (-i stdin).",
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182 metavar="FILE")
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183 parser.add_option("-n", "--numSplits", dest="numSplits", default=2, type = "int",
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184 help="The maximum number of split-read mappings to allow per read. Reads with more are excluded. Default=2",
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185 metavar="INT")
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186 parser.add_option("-d", "--includeDups", dest="includeDups", action="store_true",default=0,
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187 help="Include alignments marked as duplicates. Default=False")
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188 parser.add_option("-m", "--minNonOverlap", dest="minNonOverlap", default=20, type = "int",
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189 help="minimum non-overlap between split alignments on the query (default=20)",
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190 metavar="INT")
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191 (opts, args) = parser.parse_args()
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192 if opts.inFile is None:
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193 parser.print_help()
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194 print
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195 else:
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196 try:
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197 extractSplitsFromBwaMem(opts.inFile, opts.numSplits, opts.includeDups, opts.minNonOverlap)
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198 except IOError as err:
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199 sys.stderr.write("IOError " + str(err) + "\n");
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200 return
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201 if __name__ == "__main__":
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202 sys.exit(main())