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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
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6 __author__ = "alistair ward"
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7 __version__ = "version 0.26"
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8 __date__ = "february 2011"
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9
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10 def main():
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11 usage = "Usage: vcfPytools.py [tool] [options]\n\n" + \
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12 "Available tools:\n" + \
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13 " annotate:\n\tAnnotate the vcf file with membership in other vcf files.\n" + \
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14 " extract:\n\tExtract vcf records from a region.\n" + \
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15 " filter:\n\tFilter the vcf file.\n" + \
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16 " intersect:\n\tGenerate the intersection of two vcf files.\n" + \
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17 " merge:\n\tMerge a list of vcf files.\n" + \
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18 " multi:\n\tFind the intersections and unique fractions of multiple vcf files.\n" + \
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19 " sort:\n\tSort a vcf file.\n" + \
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20 " stats:\n\tGenerate statistics from a vcf file.\n" + \
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21 " union:\n\tGenerate the union of two vcf files.\n" + \
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22 " unique:\n\tGenerate the unique fraction from two vcf files.\n" + \
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23 " validate:\n\tValidate the input vcf file.\n\n" + \
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24 "vcfPytools.py [tool] --help for information on a specific tool."
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25
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26 # Determine the requested tool.
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27
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28 if len(sys.argv) > 1:
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29 tool = sys.argv[1]
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30 else:
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31 print >> sys.stderr, usage
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32 exit(1)
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33
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34 if tool == "annotate":
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35 import annotate
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36 success = annotate.main()
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37 elif tool == "extract":
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38 import extract
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39 success = extract.main()
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40 elif tool == "filter":
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41 import filter
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42 success = filter.main()
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43 elif tool == "intersect":
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44 import intersect
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45 success = intersect.main()
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46 elif tool == "multi":
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47 import multi
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48 success = multi.main()
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49 elif tool == "merge":
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50 import merge
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51 success = merge.main()
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52 elif tool == "sort":
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53 import sort
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54 success = sort.main()
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55 elif tool == "stats":
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56 import stats
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57 success = stats.main()
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58 elif tool == "union":
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59 import union
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60 success = union.main()
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61 elif tool == "unique":
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62 import unique
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63 success = unique.main()
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64 elif tool == "test":
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65 import test
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66 success = test.main()
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67 elif tool == "validate":
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68 import validate
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69 success = validate.main()
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70 elif tool == "--help" or tool == "-h" or tool == "?":
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71 print >> sys.stderr, usage
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72 else:
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73 print >> sys.stderr, "Unknown tool: ",tool
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74 print >> sys.stderr, "\n", usage
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75 exit(1)
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76
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77 # If program completed properly, terminate.
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78
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79 if success == 0: exit(0)
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80
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81 if __name__ == "__main__":
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82 main()
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