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1 #!/usr/bin/env python
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2
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3 tool_description = """
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4 Given coordinates of the aligned reads, calculate positions of the crosslinked
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5 nucleotides. Crosslinked nts are assumed to be one nt upstream of the 5'-end of
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6 the read.
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7
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8 By default output is written to stdout.
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9
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10 Input:
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11 * bed6 file containing coordinates of aligned reads
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12 * bed6 file containing coordinates of crosslinking events
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13
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14 Example usage:
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15 - convert read coordinates from file in.bed to coordinates of the crosslinking
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16 events, written to out.bed:
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17 coords2clnt.py in.bed --outfile out.bed
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18 """
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19
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20 epilog = """
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21 Author: Daniel Maticzka
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22 Copyright: 2015
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23 License: Apache
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24 Email: maticzkd@informatik.uni-freiburg.de
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25 Status: Testing
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26 """
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27
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28 import argparse
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29 import logging
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30 from sys import stdout
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31 from pybedtools import BedTool
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32 from pybedtools.featurefuncs import five_prime
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33 # avoid ugly python IOError when stdout output is piped into another program
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34 # and then truncated (such as piping to head)
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35 from signal import signal, SIGPIPE, SIG_DFL
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36 signal(SIGPIPE, SIG_DFL)
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37
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38 # parse command line arguments
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39 parser = argparse.ArgumentParser(description=tool_description,
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40 epilog=epilog,
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41 formatter_class=argparse.RawDescriptionHelpFormatter)
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42 # positional arguments
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43 parser.add_argument(
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44 "infile",
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45 help="Path to bed input file.")
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46 # optional arguments
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47 parser.add_argument(
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48 "-o", "--outfile",
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49 help="Write results to this file.")
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50 parser.add_argument(
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51 "-v", "--verbose",
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52 help="Be verbose.",
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53 action="store_true")
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54 parser.add_argument(
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55 "-d", "--debug",
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56 help="Print lots of debugging information",
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57 action="store_true")
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58 parser.add_argument(
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59 '--version',
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60 action='version',
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61 version='0.1.0')
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62
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63
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64 # handle arguments
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65 args = parser.parse_args()
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66 if args.debug:
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67 logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
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68 elif args.verbose:
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69 logging.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
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70 else:
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71 logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
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72 logging.info("Parsed arguments:")
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73 if args.outfile:
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74 logging.info(" outfile: enabled writing to file")
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75 logging.info(" outfile: '{}'".format(args.outfile))
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76 logging.info(" outfile: '{}'".format(args.outfile))
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77 logging.info("")
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78
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79 # data processing
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80 alns = BedTool(args.infile)
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81 clnts = alns.each(five_prime, upstream=1, downstream=0)
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82
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83 # write to file or to stdout
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84 if args.outfile:
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85 clnts.saveas(args.outfile)
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86 else:
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87 tmptool = clnts.saveas()
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88 logging.debug("results written to temporary file :" + tmptool.fn)
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89 tmp = open(tmptool.fn)
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90 for line in tmp:
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91 stdout.write(line)
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92 tmp.close()
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