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annotate utils/outconv.py @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #!/usr/bin/env python
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2 from __future__ import division
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3 from __future__ import print_function
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4 from __future__ import absolute_import
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5 from __future__ import unicode_literals
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6 import sys
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7 import argparse
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8
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9 ARG_DEFAULTS = {'input':sys.stdin}
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10 USAGE = "%(prog)s [options]"
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11 DESCRIPTION = """Split interleaved outputs of dunovo.py into pairs of paired-end files."""
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12
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13
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14 def main(argv):
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15
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16 parser = argparse.ArgumentParser(description=DESCRIPTION)
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17 parser.set_defaults(**ARG_DEFAULTS)
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18
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19 parser.add_argument('input', metavar='consensuses.fa', type=argparse.FileType('r'),
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20 help='Interleaved consensus reads (DCS or SSCS) from dunovo.py.')
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21 parser.add_argument('-1', '--out1', metavar='out_1.fa', type=argparse.FileType('w'), required=True,
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22 help='Output filename for mate 1 reads. CAUTION: Will overwrite any existing file.')
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23 parser.add_argument('-2', '--out2', metavar='out_2.fa', type=argparse.FileType('w'), required=True,
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24 help='Output filename for mate 2 reads. CAUTION: Will overwrite any existing file.')
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25
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26 args = parser.parse_args(argv[1:])
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27
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28 """
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29 SSCS:
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30 >AAAAAAAAAAAACTAAAATACAAA.ab.1 15
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31 ACTGATGAAAAGGCTGTTATTGTATCTGATGTGTAGTGTATGGCTAAGAAAAGACCTGTAATGATTTGGACTATTAGGCAGACTCCTAGAAGGGACCCAA
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32 >AAAAAAAAAAAACTAAAATACAAA.ab.2 15
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33 ATCCAAACACAACCAACATCCCCCCTAAATAAATTAAAAAAACTATTAAACCTAAAAACGATCCACCAAACCCTAAAACCATTAAACAACCAACAAACCC
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34 >AAAAAAAAAAAAGACCACGTTTCT.ab.1 15
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35 TGGAATTCAGCCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAGCAGCAACAAAATACTTCGTCACACAAGCAACAGC
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36 >AAAAAAAAAAAAGACCACGTTTCT.ba.2 18
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37 TGGAATTCAGCCTACTAGCAATTATCCCCATACTAATCAACAAAAAAAACCCACGATCAACTGAAGCAGCAACAAAATACTTCGTCACACAAGCAACAGC
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38 >AAAAAAAAAAAAGACCACGTTTCT.ab.2 15
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39 GTAGAGTTGAGTAGCGGGTAAATTTGAATTAAAATTGATAGGGGAGCAATTTTTTGTCATGTAAGAAGAATAAGTCCTATGTGCAGTGGGATCCCTTGAG
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40 >AAAAAAAAAAAAGACCACGTTTCT.ba.1 18
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41 GTAGAGTTGAGTAGCGGGTAAATTTGAATTAAAATTGATAGGGGAGCAATTTTTTGTCATGTAAGAAGAATAAGTCCTATGTGCAGTGGGATCCCTTGAG
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42
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43 DCS:
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44 >AAAAAAAACACCAAATACGCCTAC.1 28-39
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45 GCTATGAATATAGGGGCTGTAAGAATAATATAGATTATGAGGTTGAGTAGAGTGAGGGATGGGTTGTAAGGAAGAATTGCTAATATTCATCCTATGTGGG
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46 >AAAAAAAACACCAAATACGCCTAC.2 28-39
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47 TACTTCGTCACACAAGCAACAGCCTCAATAATTATCCTCCTGGCCATCGTACTCAACTATAAACAACTAGGAACATGAATATTTCAACAACAAACAAACG
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48 """
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49
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50 intype = None
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51 line_num = 0
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52 sscs_buffer = {}
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53 for line_raw in args.input:
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54 line_num += 1
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55 line = line_raw.rstrip('\r\n')
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56 if line.startswith('>'):
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57 # We're in a header line.
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58 barcode, strand, mate, famsizes = parse_header(line)
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59 if intype is None:
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60 if strand is None:
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61 intype = 'DCS'
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62 else:
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63 intype = 'SSCS'
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64 else:
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65 # We're in a sequence line.
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66 seq = line
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67 if intype == 'DCS':
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68 if mate == '1':
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69 args.out1.write('>{} {}\n{}\n'.format(barcode, famsizes, seq))
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70 elif mate == '2':
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71 args.out2.write('>{} {}\n{}\n'.format(barcode, famsizes, seq))
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72 else:
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73 fail('Error: Invalid mate "{}" on line {}.'.format(mate, line_num))
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74 elif intype == 'SSCS':
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75 # Need to get SSCS in correct order.
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76 # Collect reads until they're properly paired, then print both.
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77 if (barcode, strand) in sscs_buffer:
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78 stored_read = sscs_buffer[(barcode, strand)]
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79 new_read = {'mate':mate, 'famsizes':famsizes, 'seq':seq}
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80 if stored_read['mate'] == '1' and mate == '2':
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81 read1, read2 = stored_read, new_read
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82 elif stored_read['mate'] == '2' and mate == '1':
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83 read1, read2 = new_read, stored_read
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84 args.out1.write('>{}.{} {famsizes}\n{seq}\n'.format(barcode, strand, **read1))
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85 args.out2.write('>{}.{} {famsizes}\n{seq}\n'.format(barcode, strand, **read2))
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86 del sscs_buffer[(barcode, strand)]
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87 else:
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88 sscs_buffer[(barcode, strand)] = {'mate':mate, 'famsizes':famsizes, 'seq':seq}
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89
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90
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91 def parse_header(header):
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92 read_id, famsizes = header.split()
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93 id_fields = read_id[1:].split('.')
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94 barcode = id_fields[0]
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95 strand = None
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96 mate = id_fields[-1]
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97 if len(id_fields) == 3:
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98 strand = id_fields[1]
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99 return barcode, strand, mate, famsizes
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100
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101
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102 def fail(message):
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103 sys.stderr.write(message+"\n")
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104 sys.exit(1)
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105
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106 if __name__ == '__main__':
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107 sys.exit(main(sys.argv))