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1 #!/usr/bin/python
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2 import os
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3 import sys
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4 from optparse import OptionParser
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5
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6 OPT_DEFAULTS = {'freq_thres':0, 'covg_thres':0}
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7 BASES = ['A', 'C', 'G', 'T']
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8 USAGE = ("Usage: %prog (options) 'variant_str' ('variant_str2' (etc))\n"
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9 +" cat variants.txt > %prog (options)")
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10
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11 def main():
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12
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13 parser = OptionParser(usage=USAGE)
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14 parser.add_option('-f', '--freq-thres', dest='freq_thres', type='float',
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15 default=OPT_DEFAULTS.get('freq_thres'),
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16 help=('Frequency threshold for counting alleles, given in percentage: -f 1 '
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17 +'= 1% frequency. Default is %default%.'))
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18 parser.add_option('-c', '--covg-thres', dest='covg_thres', type='int',
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19 default=OPT_DEFAULTS.get('covg_thres'),
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20 help=('Coverage threshold. Each site must be supported by at least this '
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21 +'many reads on each strand. Otherwise the site will not be printed in '
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22 +'the output. The default is %default reads per strand.'))
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23 (options, args) = parser.parse_args()
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24 freq_thres = options.freq_thres
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25 covg_thres = options.covg_thres
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26
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27 if len(sys.argv) > 1 and '-h' in sys.argv[1][0:3]:
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28 script_name = os.path.basename(sys.argv[0])
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29 print """USAGE:
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30 $ """+script_name+""" [sample column text]
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31 $ """+script_name+""" '+A=10,+G=2,-A=20,-G=41,'
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32 $ """+script_name+""" '0/1:10,1:0.25,0.025:-A=29,-AG=1,-G=10,'
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33 $ """+script_name+""" '+A=10,+G=2,-A=20,-G=41,' '0/1:10,1:0.25,0.025:-A=29,-AG=1,-G=10,'
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34 Or invoke with no arguments to use interactively. It will read from stdin, so
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35 just paste one sample per line."""
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36 sys.exit(0)
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37
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38 if len(args) > 0:
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39 stdin = False
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40 samples = args
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41 else:
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42 stdin = True
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43 samples = sys.stdin
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44 print "Reading from standard input.."
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45
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46 for sample in samples:
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47 print ''
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48 sample = sample.split(':')[-1]
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49 if not sample:
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50 continue
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51 print sample
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52 counts_dict = parse_counts(sample)
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53 compute_stats(counts_dict, freq_thres, covg_thres)
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54
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55
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56 def parse_counts(sample_str):
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57 counts_dict = {}
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58 counts = sample_str.split(',')
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59 for count in counts:
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60 if '=' not in count:
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61 continue
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62 (var, reads) = count.split('=')
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63 if var[1:] in BASES:
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64 counts_dict[var] = int(reads)
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65 return counts_dict
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66
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67
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68 def compute_stats(counts_dict, freq_thres, covg_thres):
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69 # totals for A, C, G, T
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70 counts_unstranded = {}
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71 for base in BASES:
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72 counts_unstranded[base] = 0
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73 for strand in '+-':
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74 counts_unstranded[base] += counts_dict.get(strand+base, 0)
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75 print '+- '+str(counts_unstranded)
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76
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77 # get counts for each strand
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78 plus_counts = get_stranded_counts(counts_dict, '+')
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79 minus_counts = get_stranded_counts(counts_dict, '-')
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80 counts_lists = {'+':plus_counts, '-':minus_counts}
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81 print ' + '+str(plus_counts)
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82 print ' - '+str(minus_counts)
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83
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84 # stranded coverage threshold
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85 coverages = {}
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86 failing_strands = {}
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87 for strand in '+-':
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88 coverages[strand] = 0
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89 for count in counts_lists[strand].values():
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90 coverages[strand] += count
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91 if coverages[strand] < covg_thres:
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92 failing_strands[strand] = coverages[strand]
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93 sys.stdout.write(strand+'coverage: '+str(coverages[strand])+"\t")
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94 coverages['+-'] = coverages['+'] + coverages['-']
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95 sys.stdout.write("+-coverage: "+str(coverages['+-'])+"\n")
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96
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97 if failing_strands:
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98 for strand in failing_strands:
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99 print ('coverage on '+strand+' strand too low ('
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100 +str(failing_strands[strand])+' < '+str(covg_thres)+")")
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101 return
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102
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103 # apply frequency threshold
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104 for strand in counts_lists:
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105 strand_counts = counts_lists[strand]
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106 for variant in strand_counts.keys():
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107 # print (variant+" freq: "+str(strand_counts[variant])+"/"
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108 # +str(coverages[strand])+" = "
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109 # +str(strand_counts[variant]/float(coverages[strand])))
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110 if strand_counts[variant]/float(coverages[strand]) < freq_thres:
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111 strand_counts.pop(variant)
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112 plus_variants = sorted(plus_counts.keys())
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113 minus_variants = sorted(minus_counts.keys())
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114 if plus_variants == minus_variants:
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115 strand_bias = False
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116 print "no strand bias: +"+str(plus_variants)+" == -"+str(minus_variants)
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117 sys.stdout.write("alleles: "+str(len(plus_variants))+"\t")
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118 else:
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119 strand_bias = True
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120 print " strand bias: +"+str(plus_variants)+" != -"+str(minus_variants)
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121 sys.stdout.write("alleles: 0\t")
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122
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123 variants_sorted = sort_variants(counts_unstranded)
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124 if len(variants_sorted) >= 1:
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125 sys.stdout.write("major: "+variants_sorted[0]+"\t")
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126 minor = '.'
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127 if len(variants_sorted) == 2:
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128 minor = variants_sorted[1]
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129 elif len(variants_sorted) > 2:
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130 if (counts_unstranded.get(variants_sorted[1]) ==
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131 counts_unstranded.get(variants_sorted[2])):
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132 minor = 'N'
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133 else:
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134 minor = variants_sorted[1]
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135
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136 sys.stdout.write("minor: "+minor+"\tfreq: ")
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137 print round(float(counts_unstranded.get(minor, 0))/coverages['+-'], 5)
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138
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139
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140 def get_stranded_counts(unstranded_counts, strand):
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141 stranded_counts = {}
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142 for variant in unstranded_counts:
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143 if variant[0] == strand:
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144 stranded_counts[variant[1:]] = unstranded_counts[variant]
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145 return stranded_counts
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146
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147 def sort_variants(variant_counts):
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148 """Sort the list of variants based on their counts. Returns a list of just
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149 the variants, no counts."""
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150 variants = variant_counts.keys()
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151 var_del = []
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152 for variant in variants:
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153 if variant_counts.get(variant) == 0:
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154 var_del.append(variant)
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155 for variant in var_del:
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156 variants.remove(variant)
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157 variants.sort(reverse=True, key=lambda variant: variant_counts.get(variant,0))
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158 return variants
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159
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160 if __name__ == "__main__":
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161 main()
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