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annotate utils/sim-check.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 import re
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5 import os
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6 import sys
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7 import argparse
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8 import fastqreader
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9 script_dir = os.path.dirname(os.path.realpath(__file__))
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10 sys.path.append(os.path.dirname(script_dir))
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11 import swalign
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12
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13 CANON = 'ACGT-'
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14
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15 WGSIM_ID_REGEX = r'^(.+)_\d+_\d+_\d+:\d+:\d+_\d+:\d+:\d+_([0-9a-f]+)/[12]$'
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16 ARG_DEFAULTS = {'print_stats':True}
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17 USAGE = "%(prog)s [options]"
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18 DESCRIPTION = """Correlate (labeled) reads from duplex pipeline with truth from simulator input,
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19 and print the number of errors."""
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20
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21
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22 def main(argv):
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23
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24 parser = argparse.ArgumentParser(description=DESCRIPTION)
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25 parser.set_defaults(**ARG_DEFAULTS)
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26
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27 parser.add_argument('reads', type=argparse.FileType('r'),
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28 help='Output from duplex pipeline. Should be the tsv produced by sim-label.py.')
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29 parser.add_argument('frags', type=fastqreader.FastqReadGenerator,
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30 help='--frag-file from sim.py.')
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31 parser.add_argument('-i', '--ignore-ambiguous', action='store_true',
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32 help='Don\'t consider ambiguous bases ("N", "R", etc.) in SNV errors. Specifically, it will '
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33 'ignore any mismatch between a non-gap base in the fragment and read base that isn\'t '
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34 'one of "'+CANON+'".')
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35 parser.add_argument('-a', '--print-alignments', action='store_true',
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36 help='Print the alignments of each read with each fragment. Mostly for debug purposes.')
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37 parser.add_argument('-S', '--no-stats', dest='print_stats', action='store_false',
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38 help='Don\'t print the normal output of statistics on differences.')
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39
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40 args = parser.parse_args(argv[1:])
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41
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42 reads = iter(args.reads)
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43 frags = iter(args.frags)
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44 while True:
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45 # Read in the next output read.
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46 try:
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47 read_line = next(reads)
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48 except StopIteration:
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49 break
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50 fields = read_line.rstrip('\r\n').split('\t')
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51 assert len(fields) == 7, fields
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52 read = dict(zip(('chrom', 'frag_num', 'frag_id', 'bar', 'reads+', 'reads-', 'seq'), fields))
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53 # Read in fragments until we find the one corresponding to the output read.
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54 frag_chrom = None
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55 frag_frag_id = None
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56 while not (read['chrom'] == frag_chrom and read['frag_id'] == frag_frag_id):
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57 try:
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58 frag = next(frags)
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59 except StopIteration:
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60 break
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61 match = re.search(WGSIM_ID_REGEX, frag.id)
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62 if match:
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63 frag_chrom = match.group(1)
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64 frag_frag_id = match.group(2)
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65 else:
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66 sys.stderr.write('Invalid wgsim read name: {}\n'.format(frag.id))
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67 if frag_chrom is None and frag_frag_id is None:
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68 break
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69 # Align the output read to the fragment.
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70 align = swalign.smith_waterman_duplex(frag.seq, read['seq'])
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71 assert len(align.target) == len(align.query)
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72 if args.print_alignments:
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73 print(align.target)
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74 diffs = get_diffs(align.target, align.query, print_mid=args.print_alignments,
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75 ignore_ambig=args.ignore_ambiguous)
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76 if args.print_alignments:
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77 print(align.query)
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78 read_len = len(read['seq'])
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79 snvs = ins = dels = 0
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80 for diff in diffs:
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81 if diff['type'] == 'snv':
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82 snvs += 1
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83 elif diff['type'] == 'ins':
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84 ins += 1
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85 elif diff['type'] == 'del':
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86 dels += 1
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87 match_rate = round(align.matches/read_len, 2)
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88 if args.print_stats:
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89 print(read['bar'], read['frag_id'], read['reads+'], read['reads-'], read_len,
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90 read_len-align.matches, match_rate, len(diffs), snvs, ins, dels, sep='\t')
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91
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92
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93 def get_diffs(target, query, print_mid=False, ignore_ambig=False):
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94 diffs = []
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95 diff = None
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96 coord = 0
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97 for base1, base2 in zip(target, query):
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98 if base1 != '-':
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99 coord += 1
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100 if base1 == base2:
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101 # Finish ongoing indels and add them to the list.
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102 if diff is not None:
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103 # But omit the "indel" that's just the unaligned portion at the start.
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104 if diff['coord'] > 1:
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105 diffs.append(diff)
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106 diff = None
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107 if print_mid:
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108 sys.stdout.write('|')
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109 elif ignore_ambig and base1 != '-' and base2 not in CANON:
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110 if print_mid:
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111 sys.stdout.write(' ')
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112 elif base1 == '-':
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113 if diff is None:
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114 diff = {'coord':coord, 'type':'ins', 'alt':base2}
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115 else:
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116 diff['alt'] += base2
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117 if print_mid:
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118 sys.stdout.write(' ')
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119 elif base2 == '-':
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120 if diff is None:
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121 diff = {'coord':coord-1, 'type':'del', 'alt':1}
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122 else:
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123 diff['alt'] += 1
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124 if print_mid:
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125 sys.stdout.write(' ')
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126 else:
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127 diffs.append({'coord':coord, 'type':'snv', 'alt':base2})
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128 if print_mid:
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129 sys.stdout.write(' ')
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130 if diff is not None:
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131 diffs.append(diff)
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132 if print_mid:
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133 print()
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134 return diffs
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135
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136
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137 def fail(message):
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138 sys.stderr.write(message+"\n")
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139 sys.exit(1)
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140
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141 if __name__ == '__main__':
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142 sys.exit(main(sys.argv))