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annotate utils/stats.py @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents af383638de66
children
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4
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1 #!/usr/bin/env python
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2 from __future__ import division
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3 import os
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4 import sys
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5 import math
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6 import argparse
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7 sys.path.append(os.path.dirname(os.path.dirname(os.path.realpath(__file__))))
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8 import seqtools
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9 import swalign
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10
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11 INF = float('inf')
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12 STATS = ('diffs', 'diffs-binned', 'seqlen', 'strand')
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13 OPT_DEFAULTS = {'bins':10, 'probes':'', 'thres':0.75}
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14 USAGE = "%(prog)s [options]"
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15 DESCRIPTION = """"""
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16
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17
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18 def main(argv):
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19
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20 parser = argparse.ArgumentParser(description=DESCRIPTION)
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21 parser.set_defaults(**OPT_DEFAULTS)
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22
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23 parser.add_argument('stats',
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24 help='The type of statistics to compute and print. Give a comma-separated list of stat names, '
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25 'choosing from "{}".'.format('", "'.join(STATS)))
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26 parser.add_argument('infile', metavar='read-families.msa.tsv', nargs='?',
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27 help='The --msa output of sscs.py. Will read from stdin if not provided.')
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28 parser.add_argument('-b', '--bins', type=int,
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29 help='The number of bins to segment reads into when doing "diffs-binned".')
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30 parser.add_argument('-p', '--probes',
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31 help='Sequence excerpts from the sense strand. Required for "strand" statistic. '
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32 'Comma-separated.')
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33 parser.add_argument('-t', '--thres', type=int,
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34 help='Alignment identity threshold (in fraction, not decimal). Default: %(default)s')
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35
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36 args = parser.parse_args(argv[1:])
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37
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38 stats = args.stats.split(',')
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39 for stat in stats:
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40 if stat not in STATS:
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41 fail('Error: invalid statistic "{}". Must choose one of "{}".'.format(stat, '", "'.join(STATS)))
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42 if 'strand' in stats and not args.probes:
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43 fail('Error: must provide a probe if requesting "strand" statistic.')
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44
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45 if args.infile:
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46 infile = open(args.infile)
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47 else:
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48 infile = sys.stdin
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49
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50 family = []
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51 consensus = None
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52 barcode = None
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53 for line in infile:
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54 fields = line.rstrip('\r\n').split('\t')
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55 if len(fields) != 3:
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56 continue
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57 (this_barcode, name, seq) = fields
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58 if fields[1] == 'CONSENSUS':
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59 if family and consensus:
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60 process_family(stats, barcode, consensus, family, args)
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61 barcode = this_barcode
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62 consensus = seq
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63 family = []
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64 else:
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65 family.append(seq)
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66 if family and consensus:
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67 process_family(stats, barcode, consensus, family, args)
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68
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69 if infile is not sys.stdin:
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70 infile.close()
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71
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72
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73 #TODO: Maybe print the number of N's in the consensus?
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74 def process_family(stats, barcode, consensus, family, args):
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75 # Compute stats requiring the whole family at once.
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76 for stat in stats:
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77 if stat == 'diffs':
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78 diffs = seqtools.get_diffs_frac_simple(consensus, family)
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79 elif stat == 'diffs-binned':
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80 diffs_binned = seqtools.get_diffs_frac_binned(consensus, family, args.bins)
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81 elif stat == 'strand':
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82 probes = args.probes.split(',')
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83 strand = get_strand(consensus, probes, args.thres)
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84 # Print the requested stats for each read.
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85 # Columns: barcode, [stat columns], read sequence.
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86 for (i, read) in enumerate(family):
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87 sys.stdout.write(barcode+'\t')
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88 for stat in stats:
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89 if stat == 'diffs':
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90 sys.stdout.write('{}\t'.format(round_sig_figs(diffs[i], 3)))
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91 elif stat == 'diffs-binned':
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92 if diffs_binned is None:
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93 sys.stdout.write('\t' * args.bins)
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94 else:
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95 for diff in diffs_binned[i]:
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96 sys.stdout.write(str(round_sig_figs(diff, 3))+'\t')
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97 elif stat == 'seqlen':
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98 sys.stdout.write('{}\t'.format(len(read)))
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99 elif stat == 'strand':
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100 sys.stdout.write('{}\t'.format(strand))
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101 print read.upper()
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102
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103
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104 def get_strand(seq, probes, thres):
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105 """Determine which strand the sequence comes from by trying to align probes from the sense strand.
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106 Returns 'sense', 'anti', or None.
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107 Algorithm: This tries each probe in both directions.
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108 If at least one of the alignments has an identity above the threshold, a vote is cast for the
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109 direction with a higher identity.
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110 If the votes that were cast are unanimous for one direction, that strand is returned.
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111 Else, return None."""
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112 votes = []
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113 for probe in probes:
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114 alignment = swalign.smith_waterman(seq, probe)
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115 sense_id = alignment.matches/len(probe)
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116 alignment = swalign.smith_waterman(seq, seqtools.get_revcomp(probe))
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117 anti_id = alignment.matches/len(probe)
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118 # print '{}: sense: {}, anti: {}'.format(probe, sense_id, anti_id)
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119 if sense_id > thres or anti_id > thres:
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120 if sense_id > anti_id:
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121 votes.append('sense')
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122 else:
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123 votes.append('anti')
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124 strand = None
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125 for vote in votes:
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126 if strand:
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127 if strand != vote:
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128 return None
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129 else:
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130 strand = vote
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131 return strand
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132
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133
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134 def round_sig_figs(n, figs):
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135 if n == 0:
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136 return n
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137 elif n < 0:
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138 n = -n
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139 sign = -1
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140 elif n > 0:
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141 sign = 1
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142 elif math.isnan(n) or n == INF:
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143 return n
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144 magnitude = int(math.floor(math.log10(n)))
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145 return sign * round(n, figs - 1 - magnitude)
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146
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147
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148 def fail(message):
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149 sys.stderr.write(message+"\n")
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150 sys.exit(1)
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151
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152
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153 if __name__ == '__main__':
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154 sys.exit(main(sys.argv))