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1 #!/usr/bin/python
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2
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3 import os.path
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4 import sys
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5 import optparse
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6
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7 import bedClass
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8 from bedClass import *
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9
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10 import vcfClass
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11 from vcfClass import *
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12
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13 import tools
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14 from tools import *
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15
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16 if __name__ == "__main__":
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17 main()
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18
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19 # Intersect two vcf files. It is assumed that the two files are
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20 # sorted by genomic coordinates and the reference sequences are
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21 # in the same order.
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22 def intersectVcf(v1, v2, priority, outputFile):
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23 success1 = v1.getRecord()
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24 success2 = v2.getRecord()
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25 currentReferenceSequence = v1.referenceSequence
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26
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27 # As soon as the end of either file is reached, there can be no
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28 # more intersecting SNPs, so terminate.
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29 while success1 and success2:
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30 if v1.referenceSequence == v2.referenceSequence and v1.referenceSequence == currentReferenceSequence:
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31 if v1.position == v2.position:
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32 writeVcfRecord(priority, v1, v2, outputFile)
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33 success1 = v1.getRecord()
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34 success2 = v2.getRecord()
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35 elif v2.position > v1.position: success1 = v1.parseVcf(v2.referenceSequence, v2.position, False, None)
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36 elif v1.position > v2.position: success2 = v2.parseVcf(v1.referenceSequence, v1.position, False, None)
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37 else:
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38 if v1.referenceSequence == currentReferenceSequence: success1 = v1.parseVcf(v2.referenceSequence, v2.position, False, None)
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39 elif v2.referenceSequence == currentReferenceSequence: success2 = v2.parseVcf(v1.referenceSequence, v1.position, False, None)
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40
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41 # If the last record for a reference sequence is the same for both vcf
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42 # files, they will both have referenceSequences different from the
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43 # current reference sequence. Change the reference sequence to reflect
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44 # this and proceed.
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45 else:
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46 if v1.referenceSequence != v2.referenceSequence:
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47 print >> sys.stderr, "ERROR: Reference sequences for both files are unexpectedly different."
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48 print >> sys.stderr, "Check that both files contain records for the following reference sequences:"
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49 print >> sys.stderr, "\t", v1.referenceSequence, " and ", v2.referenceSequence
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50 exit(1)
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51 currentReferenceSequence = v1.referenceSequence
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52
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53 # Intersect a vcf file and a bed file. It is assumed that the
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54 # two files are sorted by genomic coordinates and the reference
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55 # sequences are in the same order.
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56 def intersectVcfBed(v, b, outputFile):
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57 successb = b.getRecord()
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58 successv = v.getRecord()
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59 currentReferenceSequence = v.referenceSequence
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60
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61 # As soon as the end of the first file is reached, there are no
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62 # more intersections and the program can terminate.
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63 while successv:
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64 if v.referenceSequence == b.referenceSequence:
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65 if v.position < b.start: successv = v.parseVcf(b.referenceSequence, b.start, False, None)
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66 elif v.position > b.end: successb = b.parseBed(v.referenceSequence, v.position)
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67 else:
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68 outputFile.write(v.record)
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69 successv = v.getRecord()
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70 else:
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71 if v.referenceSequence == currentReferenceSequence: successv = v.parseVcf(b.referenceSequence, b.start, False, None)
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72 if b.referenceSequence == currentReferenceSequence: successb = b.parseBed(v.referenceSequence, v.position)
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73 currentReferenceSequence = v.referenceSequence
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74
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75 def main():
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76
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77 # Parse the command line options
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78 usage = "Usage: vcfPytools.py intersect [options]"
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79 parser = optparse.OptionParser(usage = usage)
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80 parser.add_option("-i", "--in",
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81 action="append", type="string",
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82 dest="vcfFiles", help="input vcf files")
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83 parser.add_option("-b", "--bed",
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84 action="store", type="string",
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85 dest="bedFile", help="input bed vcf file")
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86 parser.add_option("-o", "--out",
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87 action="store", type="string",
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88 dest="output", help="output vcf file")
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89 parser.add_option("-f", "--priority-file",
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90 action="store", type="string",
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91 dest="priorityFile", help="output records from this vcf file")
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92
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93 (options, args) = parser.parse_args()
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94
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95 # Check that a single vcf file is given.
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96 if options.vcfFiles == None:
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97 parser.print_help()
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98 print >> sys.stderr, "\nAt least one vcf file (--in, -i) is required for performing intersection."
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99 exit(1)
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100 elif len(options.vcfFiles) > 2:
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101 parser.print_help()
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102 print >> sys.stderr, "\nAt most, two vcf files (--in, -i) can be submitted for performing intersection."
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103 exit(1)
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104 elif len(options.vcfFiles) == 1 and not options.bedFile:
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105 parser.print_help()
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106 print >> sys.stderr, "\nIf only one vcf file (--in, -i) is specified, a bed file is also required for performing intersection."
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107 exit(1)
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108
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109 # Set the output file to stdout if no output file was specified.
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110 outputFile, writeOut = setOutput(options.output) # tools.py
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111
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112 # If intersecting with a bed file, call the bed intersection routine.
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113 if options.bedFile:
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114 v = vcf() # Define vcf object.
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115 b = bed() # Define bed object.
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116
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117 # Open the files.
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118 v.openVcf(options.vcfFiles[0])
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119 b.openBed(options.bedFile)
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120
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121 # Read in the header information.
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122 v.parseHeader(options.vcfFiles[0], writeOut)
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123 taskDescriptor = "##vcfPytools=intersect " + options.vcfFiles[0] + ", " + options.bedFile
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124 writeHeader(outputFile, v, False, taskDescriptor) # tools.py
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125
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126 # Intersect the vcf file with the bed file.
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127 intersectVcfBed(v, b, outputFile)
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128
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129 # Check that the input files had the same list of reference sequences.
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130 # If not, it is possible that there were some problems.
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131 checkReferenceSequenceLists(v.referenceSequenceList, b.referenceSequenceList) # tools.py
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132
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133 # Close the files.
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134 v.closeVcf(options.vcfFiles[0])
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135 b.closeBed(options.bedFile)
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136
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137 else:
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138 priority = setVcfPriority(options.priorityFile, options.vcfFiles)
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139 v1 = vcf() # Define vcf object.
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140 v2 = vcf() # Define vcf object.
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141
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142 # Open the vcf files.
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143 v1.openVcf(options.vcfFiles[0])
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144 v2.openVcf(options.vcfFiles[1])
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145
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146 # Read in the header information.
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147 v1.parseHeader(options.vcfFiles[0], writeOut)
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148 v2.parseHeader(options.vcfFiles[1], writeOut)
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149 if priority == 3:
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150 v3 = vcf() # Generate a new vcf object that will contain the header information of the new file.
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151 mergeHeaders(v1, v2, v3) # tools.py
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152 v1.processInfo = True
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153 v2.processInfo = True
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154 else: checkDataSets(v1, v2)
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155
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156 #print v1.samplesList
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157 #print v2.samplesList
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158
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159 # Check that the header for the two files contain the same samples.
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160 if v1.samplesList != v2.samplesList:
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161 print >> sys.stderr, "vcf files contain different samples (or sample order)."
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162 exit(1)
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163 else:
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164 taskDescriptor = "##vcfPytools=intersect " + v1.filename + ", " + v2.filename
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165 if priority == 3: writeHeader(outputFile, v3, False, taskDescriptor)
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166 elif (priority == 2 and v2.hasHeader) or not v1.hasHeader: writeHeader(outputFile, v2, False, taskDescriptor) # tools.py
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167 else: writeHeader(outputFile, v1, False, taskDescriptor) # tools.py
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168
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169 # Intersect the two vcf files.
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170 intersectVcf(v1, v2, priority, outputFile)
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171
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172 # Check that the input files had the same list of reference sequences.
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173 # If not, it is possible that there were some problems.
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174 checkReferenceSequenceLists(v1.referenceSequenceList, v2.referenceSequenceList) # tools.py
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175
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176 # Close the vcf files.
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177 v1.closeVcf(options.vcfFiles[0])
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178 v2.closeVcf(options.vcfFiles[1])
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179
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180 # End the program.
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181 return 0
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