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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 string import maketrans
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6 from sys import stdout
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7 from Bio import SeqIO
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8 from Bio.Seq import Seq
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9 from Bio.Alphabet import IUPAC
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10
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2
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11 tool_description = """
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12 Convert standard nucleotides to IUPAC nucleotide codes used for binary barcodes.
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13
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14 A and G are converted to nucleotide code R. T, U and C are converted to Y. By
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15 default output is written to stdout.
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16
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17 Example usage:
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18 - write converted sequences from file in.fa to file file out.fa:
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19 convert_bc_to_binary_RY.py in.fa --outfile out.fa
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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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8
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37 help="Path to fastq input file.")
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2
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38 # optional arguments
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39 parser.add_argument(
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40 "-o", "--outfile",
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41 help="Write results to this file.")
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42 parser.add_argument(
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8
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43 "--fasta-format",
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44 dest="fasta_format",
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45 help="Read and write fasta instead of fastq format.",
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46 action="store_true")
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47 parser.add_argument(
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2
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48 "-v", "--verbose",
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49 help="Be verbose.",
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50 action="store_true")
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51 parser.add_argument(
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52 "-d", "--debug",
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53 help="Print lots of debugging information",
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54 action="store_true")
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55 parser.add_argument(
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56 '--version',
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57 action='version',
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58 version='0.1.0')
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59
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60
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61 def translate_nt_to_RY(seq):
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62 """Translates nucleotides to RY (A,G -> R; C,U,T -> Y).
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63
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64 >>> translate_nt_to_RY("ACGUTACGUT")
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65 RYRYYRYRYY
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66 """
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67 trans_table = maketrans("AGCUT", "RRYYY")
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68 trans_seq = seq.translate(trans_table)
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69 logging.debug(seq + " -> " + trans_seq)
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70 return trans_seq
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71
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72
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73 def translate_nt_to_RY_iterator(robj):
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74 """Translate SeqRecords sequences to RY alphabet."""
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75 for record in robj:
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8
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76 if not args.fasta_format:
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77 saved_letter_annotations = record.letter_annotations
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78 record.letter_annotations = {}
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2
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79 record.seq = Seq(translate_nt_to_RY(str(record.seq)),
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80 IUPAC.unambiguous_dna)
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8
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81 if not args.fasta_format:
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82 record.letter_annotations = saved_letter_annotations
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2
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83 yield record
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84
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85 # handle arguments
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86 args = parser.parse_args()
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87 if args.debug:
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88 logging.basicConfig(level=logging.DEBUG, format="%(asctime)s - %(filename)s - %(levelname)s - %(message)s")
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89 elif args.verbose:
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90 logging.basicConfig(level=logging.INFO, format="%(filename)s - %(levelname)s - %(message)s")
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91 else:
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92 logging.basicConfig(format="%(filename)s - %(levelname)s - %(message)s")
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93 logging.info("Parsed arguments:")
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94 if args.outfile:
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95 logging.info(" outfile: enabled writing to file")
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96 logging.info(" outfile: '{}'".format(args.outfile))
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97 logging.info(" outfile: '{}'".format(args.outfile))
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98 logging.info("")
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99
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100 # get input iterator
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101 input_handle = open(args.infile, "rU")
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8
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102 if args.fasta_format:
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103 input_seq_iterator = SeqIO.parse(input_handle, "fasta")
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104 else:
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105 input_seq_iterator = SeqIO.parse(input_handle, "fastq")
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2
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106 convert_seq_iterator = translate_nt_to_RY_iterator(input_seq_iterator)
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107 output_handle = (open(args.outfile, "w") if args.outfile is not None else stdout)
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8
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108 if args.fasta_format:
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109 SeqIO.write(convert_seq_iterator, output_handle, "fasta")
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110 else:
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111 SeqIO.write(convert_seq_iterator, output_handle, "fastq")
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2
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112 output_handle.close()
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