--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/vcf_tools/intersect.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,181 @@
+#!/usr/bin/python
+
+import os.path
+import sys
+import optparse
+
+import bedClass
+from bedClass import *
+
+import vcfClass
+from vcfClass import *
+
+import tools
+from tools import *
+
+if __name__ == "__main__":
+  main()
+
+# Intersect two vcf files.  It is assumed that the two files are
+# sorted by genomic coordinates and the reference sequences are
+# in the same order.
+def intersectVcf(v1, v2, priority, outputFile):
+  success1 = v1.getRecord()
+  success2 = v2.getRecord()
+  currentReferenceSequence = v1.referenceSequence
+
+# As soon as the end of either file is reached, there can be no
+# more intersecting SNPs, so terminate.
+  while success1 and success2:
+    if v1.referenceSequence == v2.referenceSequence and v1.referenceSequence == currentReferenceSequence:
+      if v1.position == v2.position:
+        writeVcfRecord(priority, v1, v2, outputFile)
+        success1 = v1.getRecord()
+        success2 = v2.getRecord()
+      elif v2.position > v1.position: success1 = v1.parseVcf(v2.referenceSequence, v2.position, False, None)
+      elif v1.position > v2.position: success2 = v2.parseVcf(v1.referenceSequence, v1.position, False, None)
+    else:
+      if v1.referenceSequence == currentReferenceSequence: success1 = v1.parseVcf(v2.referenceSequence, v2.position, False, None)
+      elif v2.referenceSequence == currentReferenceSequence: success2 = v2.parseVcf(v1.referenceSequence, v1.position, False, None)
+
+# If the last record for a reference sequence is the same for both vcf
+# files, they will both have referenceSequences different from the
+# current reference sequence.  Change the reference sequence to reflect
+# this and proceed.
+      else:
+        if v1.referenceSequence != v2.referenceSequence:
+          print >> sys.stderr, "ERROR: Reference sequences for both files are unexpectedly different."
+          print >> sys.stderr, "Check that both files contain records for the following reference sequences:"
+          print >> sys.stderr, "\t", v1.referenceSequence, " and ", v2.referenceSequence
+          exit(1)
+      currentReferenceSequence = v1.referenceSequence
+
+# Intersect a vcf file and a bed file.  It is assumed that the 
+# two files are sorted by genomic coordinates and the reference
+# sequences are in the same order.
+def intersectVcfBed(v, b, outputFile):
+  successb = b.getRecord()
+  successv = v.getRecord()
+  currentReferenceSequence = v.referenceSequence
+
+# As soon as the end of the first file is reached, there are no
+# more intersections and the program can terminate.
+  while successv:
+    if v.referenceSequence == b.referenceSequence:
+      if v.position < b.start: successv = v.parseVcf(b.referenceSequence, b.start, False, None)
+      elif v.position > b.end: successb = b.parseBed(v.referenceSequence, v.position)
+      else:
+        outputFile.write(v.record)
+        successv = v.getRecord()
+    else:
+      if v.referenceSequence == currentReferenceSequence: successv = v.parseVcf(b.referenceSequence, b.start, False, None)
+      if b.referenceSequence == currentReferenceSequence: successb = b.parseBed(v.referenceSequence, v.position)
+      currentReferenceSequence = v.referenceSequence
+
+def main():
+
+# Parse the command line options
+  usage = "Usage: vcfPytools.py intersect [options]"
+  parser = optparse.OptionParser(usage = usage)
+  parser.add_option("-i", "--in",
+                    action="append", type="string",
+                    dest="vcfFiles", help="input vcf files")
+  parser.add_option("-b", "--bed",
+                    action="store", type="string",
+                    dest="bedFile", help="input bed vcf file")
+  parser.add_option("-o", "--out",
+                    action="store", type="string",
+                    dest="output", help="output vcf file")
+  parser.add_option("-f", "--priority-file",
+                    action="store", type="string",
+                    dest="priorityFile", help="output records from this vcf file")
+
+  (options, args) = parser.parse_args()
+
+# Check that a single  vcf file is given.
+  if options.vcfFiles == None:
+    parser.print_help()
+    print >> sys.stderr, "\nAt least one vcf file (--in, -i) is required for performing intersection."
+    exit(1)
+  elif len(options.vcfFiles) > 2:
+    parser.print_help()
+    print >> sys.stderr, "\nAt most, two vcf files (--in, -i) can be submitted for performing intersection."
+    exit(1)
+  elif len(options.vcfFiles) == 1 and not options.bedFile:
+    parser.print_help()
+    print >> sys.stderr, "\nIf only one vcf file (--in, -i) is specified, a bed file is also required for performing intersection."
+    exit(1)
+
+# Set the output file to stdout if no output file was specified.
+  outputFile, writeOut = setOutput(options.output) # tools.py
+
+# If intersecting with a bed file, call the bed intersection routine.
+  if options.bedFile:
+    v = vcf() # Define vcf object.
+    b = bed() # Define bed object.
+
+# Open the files.
+    v.openVcf(options.vcfFiles[0])
+    b.openBed(options.bedFile)
+
+# Read in the header information.
+    v.parseHeader(options.vcfFiles[0], writeOut)
+    taskDescriptor = "##vcfPytools=intersect " + options.vcfFiles[0] + ", " + options.bedFile
+    writeHeader(outputFile, v, False, taskDescriptor) # tools.py
+
+# Intersect the vcf file with the bed file.
+    intersectVcfBed(v, b, outputFile)
+
+# Check that the input files had the same list of reference sequences.
+# If not, it is possible that there were some problems.
+    checkReferenceSequenceLists(v.referenceSequenceList, b.referenceSequenceList) # tools.py
+
+# Close the files.
+    v.closeVcf(options.vcfFiles[0])
+    b.closeBed(options.bedFile)
+
+  else:
+    priority = setVcfPriority(options.priorityFile, options.vcfFiles)
+    v1 = vcf() # Define vcf object.
+    v2 = vcf() # Define vcf object.
+
+# Open the vcf files.
+    v1.openVcf(options.vcfFiles[0])
+    v2.openVcf(options.vcfFiles[1])
+
+# Read in the header information.
+    v1.parseHeader(options.vcfFiles[0], writeOut)
+    v2.parseHeader(options.vcfFiles[1], writeOut)
+    if priority == 3:
+      v3 = vcf() # Generate a new vcf object that will contain the header information of the new file.
+      mergeHeaders(v1, v2, v3) # tools.py
+      v1.processInfo = True
+      v2.processInfo = True
+    else: checkDataSets(v1, v2)
+    
+    #print v1.samplesList
+    #print v2.samplesList
+
+# Check that the header for the two files contain the same samples.
+    if v1.samplesList != v2.samplesList:
+      print >> sys.stderr, "vcf files contain different samples (or sample order)."
+      exit(1)
+    else:
+      taskDescriptor = "##vcfPytools=intersect " + v1.filename + ", " + v2.filename
+      if priority == 3: writeHeader(outputFile, v3, False, taskDescriptor)
+      elif (priority == 2 and v2.hasHeader) or not v1.hasHeader: writeHeader(outputFile, v2, False, taskDescriptor) # tools.py
+      else: writeHeader(outputFile, v1, False, taskDescriptor) # tools.py
+
+# Intersect the two vcf files.
+    intersectVcf(v1, v2, priority, outputFile)
+
+# Check that the input files had the same list of reference sequences.
+# If not, it is possible that there were some problems.
+    checkReferenceSequenceLists(v1.referenceSequenceList, v2.referenceSequenceList) # tools.py
+
+# Close the vcf files.
+    v1.closeVcf(options.vcfFiles[0])
+    v2.closeVcf(options.vcfFiles[1])
+
+# End the program.
+  return 0