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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 sys import stdout
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6 from Bio.SeqIO.QualityIO import FastqGeneralIterator
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7 # avoid ugly python IOError when stdout output is piped into another program
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8 # and then truncated (such as piping to head)
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9 from signal import signal, SIGPIPE, SIG_DFL
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10 signal(SIGPIPE, SIG_DFL)
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11
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2
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12 tool_description = """
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13 Remove a certain number of nucleotides from the 3'-tails of sequences in fastq
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14 format.
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15
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16 Example usage:
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17 - remove the last 7 nucleotides from file input.fastq, write result to file
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18 output.fastq:
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19 remove_tail.py input.fastq 7 --out output.fastq
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20 """
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21
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22 epilog = """
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23 Author: Daniel Maticzka
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24 Copyright: 2015
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25 License: Apache
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26 Email: maticzkd@informatik.uni-freiburg.de
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27 Status: Testing
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28 """
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29
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30 # parse command line arguments
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31 parser = argparse.ArgumentParser(description=tool_description,
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32 epilog=epilog,
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33 formatter_class=argparse.RawDescriptionHelpFormatter)
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34 # positional arguments
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35 parser.add_argument(
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36 "infile",
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37 help="Path to fastq file.")
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38 parser.add_argument(
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39 "length",
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40 type=int,
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41 help="Remove this many nts.")
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42 # optional arguments
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43 parser.add_argument(
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44 "-o", "--outfile",
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45 help="Write results to this file.")
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46 parser.add_argument(
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47 "-v", "--verbose",
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48 help="Be verbose.",
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49 action="store_true")
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50 parser.add_argument(
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51 "-d", "--debug",
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52 help="Print lots of debugging information",
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53 action="store_true")
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54 parser.add_argument(
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55 '--version',
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56 action='version',
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57 version='0.1.0')
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58
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59 args = parser.parse_args()
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60 if args.debug:
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61 logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
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62 elif args.verbose:
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63 logging.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
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64 else:
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65 logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
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66 logging.info("Parsed arguments:")
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67 logging.info(" infile: '{}'".format(args.infile))
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68 logging.info(" length: '{}'".format(args.length))
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69 if args.outfile:
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70 logging.info(" outfile: enabled writing to file")
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71 logging.info(" outfile: '{}'".format(args.outfile))
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72 logging.info("")
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73
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74 # check length parameter
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75 if args.length < 0:
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76 raise ValueError("Length must be a positive integer, is '{}'.".format(args.length))
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77
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78 # remove tail
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79 with (open(args.outfile, "w") if args.outfile is not None else stdout) as samout:
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80 for header, seq, qual in FastqGeneralIterator(open(args.infile)):
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81
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82 # if removing tail would lead to an empty sequence,
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83 # set sequence to a single N to keep fastq synchronized
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84 if len(seq) <= args.length:
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85 seq = "N"
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86 qual = "B"
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87 logging.debug("read '{}' was too short to remove full tail".format(header))
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88 logging.debug("seq: {}".format(seq))
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89 logging.debug("len(seq): {}".format(len(seq)))
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90 else:
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91 seq = seq[0:-args.length]
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92 qual = qual[0:-args.length]
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93
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94 samout.write("@%s\n%s\n+\n%s\n" % (header, seq, qual))
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