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1 #!/usr/bin/env python
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2
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50
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3 import argparse
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4 import logging
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5 from subprocess import check_call
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6 import os
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7
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2
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8 tool_description = """
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9 Remove spurious events originating from errors in random sequence tags.
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10
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11 This script compares all events sharing the same coordinates. Among each group
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12 of events the maximum number of PCR duplicates is determined. All events that
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13 are supported by less than 10 percent of this maximum count are removed.
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14
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15 Input:
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16 * bed6 file containing crosslinking events with score field set to number of PCR
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17 duplicates
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18
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19 Output:
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20 * bed6 file with spurious crosslinking events removed, sorted by fields chrom,
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21 start, stop, strand
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22
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23 Example usage:
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24 - remove spurious events from spurious.bed and write results to file cleaned.bed
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50
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25 rm_spurious_events.py spurious.bed --oufile cleaned.bed
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2
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26 """
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27
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28 epilog = """
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29 Author: Daniel Maticzka
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30 Copyright: 2015
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31 License: Apache
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32 Email: maticzkd@informatik.uni-freiburg.de
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33 Status: Testing
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34 """
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35
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36
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37 class DefaultsRawDescriptionHelpFormatter(argparse.ArgumentDefaultsHelpFormatter,
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38 argparse.RawDescriptionHelpFormatter):
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39 # To join the behaviour of RawDescriptionHelpFormatter with that of ArgumentDefaultsHelpFormatter
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40 pass
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41
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42
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50
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43 def main():
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44 # parse command line arguments
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45 parser = argparse.ArgumentParser(description=tool_description,
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46 epilog=epilog,
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47 formatter_class=DefaultsRawDescriptionHelpFormatter)
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48 # positional arguments
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49 parser.add_argument(
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50 "events",
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51 help="Path to bed6 file containing alignments.")
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52 # optional arguments
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53 parser.add_argument(
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54 "-o", "--outfile",
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55 required=True,
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56 help="Write results to this file.")
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57 parser.add_argument(
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58 "-t", "--threshold",
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59 type=float,
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60 default=0.1,
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61 help="Threshold for spurious event removal."
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62 )
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63 # misc arguments
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64 parser.add_argument(
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65 "-v", "--verbose",
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66 help="Be verbose.",
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67 action="store_true")
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68 parser.add_argument(
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69 "-d", "--debug",
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70 help="Print lots of debugging information",
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71 action="store_true")
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72 parser.add_argument(
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73 '--version',
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74 action='version',
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75 version='0.1.0')
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2
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76
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77 args = parser.parse_args()
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2
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78
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79 if args.debug:
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80 logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
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81 elif args.verbose:
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82 logging.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
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83 else:
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84 logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
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85 logging.info("Parsed arguments:")
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86 logging.info(" alignments: '{}'".format(args.events))
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87 logging.info(" threshold: '{}'".format(args.threshold))
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88 if args.outfile:
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89 logging.info(" outfile: enabled writing to file")
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90 logging.info(" outfile: '{}'".format(args.outfile))
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91 logging.info("")
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2
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92
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50
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93 # check threshold parameter value
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94 if args.threshold < 0 or args.threshold > 1:
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95 raise ValueError("Threshold must be in [0,1].")
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96
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97 if not os.path.isfile(args.events):
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98 raise Exception("ERROR: file '{}' not found.")
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99
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100 # prepare barcode library
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101 syscall = "cat " + args.events + " | sort -k1,1V -k6,6 -k2,2n -k3,3 -k5,5nr | perl " + os.path.dirname(os.path.realpath(__file__)) + "/rm_spurious_events.pl --frac_max " + str(args.threshold) + "| sort -k1,1V -k2,2n -k3,3n -k6,6 -k4,4 -k5,5nr > " + args.outfile
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102 check_call(syscall, shell=True)
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103
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104
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105 if __name__ == "__main__":
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106 main()
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