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1 #!/usr/bin/python
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2
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3 import re
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4 import sys
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5 import optparse
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6 import csv
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7 import re
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8 import pprint
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9 from decimal import *
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10 from rpy import *
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11
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12 def main():
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13 csv.field_size_limit(1000000000)
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14
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15 parser = optparse.OptionParser()
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16 parser.add_option('-v', '--sample_vcf', dest = 'sample_vcf', action = 'store', type = 'string', default = None, help = "Sample VCF from GATK Unified Genotyper")
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17 parser.add_option('-l', '--loess_span', dest = 'loess_span', action = 'store', type = 'float', default = .01, help = "Loess span")
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18 parser.add_option('-d', '--d_yaxis', dest = 'd_yaxis', action = 'store', type = 'float', default = .7, help = "y-axis upper limit for dot plot")
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19 parser.add_option('-y', '--h_yaxis', dest = 'h_yaxis', action = 'store', type = 'int', default = 5, help = "y-axis upper limit for histogram plot")
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20 parser.add_option('-c', '--points_color', dest = 'points_color', action = 'store', type = 'string', default = "gray27", help = "Color for data points")
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21 parser.add_option('-k', '--loess_color', dest = 'loess_color', action = 'store', type = 'string', default = "red", help = "Color for loess regression line")
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22 parser.add_option('-z', '--standardize', dest = 'standardize', default= 'true', help = "Standardize X-axis")
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23 parser.add_option('-b', '--break_file', dest = 'break_file', action = 'store', type = 'string', default = 'C.elegans', help = "File defining the breaks per chromosome")
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24 parser.add_option('-x', '--bin_size', dest = 'bin_size', action = 'store', type = 'int', default = 1000000, help = "Size of histogram bins, default is 1mb")
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25 parser.add_option('-n', '--normalize_bins', dest = 'normalize_bins', default= 'true', help = "Normalize histograms")
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26
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27
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28 parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name")
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29 parser.add_option('-s', '--location_plot_output', dest = 'location_plot_output', action = 'store', type = 'string', default = "SNP_Mapping_Plot.pdf", help = "Output file name of SNP plots by chromosomal location")
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30
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31 (options, args) = parser.parse_args()
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32
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33 vcf_info = parse_vcf(sample_vcf = options.sample_vcf)
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34
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35 output_vcf_info(output = options.output, vcf_info = vcf_info)
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36
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37 #output plot with all ratios
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38 rounded_bin_size = int(round((float(options.bin_size) / 1000000), 1) * 1000000)
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39
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40 normalized_histogram_bins_per_mb = calculate_normalized_histogram_bins_per_xbase(vcf_info = vcf_info, xbase = rounded_bin_size, normalize_bins = options.normalize_bins)
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41 normalized_histogram_bins_per_5kb = calculate_normalized_histogram_bins_per_xbase(vcf_info = vcf_info, xbase = (rounded_bin_size / 2), normalize_bins = options.normalize_bins)
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42
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43 break_dict = parse_breaks(break_file = options.break_file)
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44
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45 output_scatter_plots_by_location(location_plot_output = options.location_plot_output, vcf_info = vcf_info, loess_span=options.loess_span, d_yaxis=options.d_yaxis, h_yaxis=options.h_yaxis, points_color=options.points_color, loess_color=options.loess_color, standardize =options.standardize, normalized_hist_per_mb = normalized_histogram_bins_per_mb, normalized_hist_per_5kb = normalized_histogram_bins_per_5kb, breaks = break_dict, rounded_bin_size = rounded_bin_size)
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46
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47
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48 def skip_headers(reader = None, i_file = None):
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49 # count headers
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50 comment = 0
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51 while reader.next()[0].startswith('#'):
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52 comment = comment + 1
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53
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54 # skip headers
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55 i_file.seek(0)
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56 for i in range(0, comment):
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57 reader.next()
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58
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59 def parse_breaks(break_file = None):
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60 if break_file == 'C.elegans':
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61 break_dict = { 'I' : 16 , 'II' : 16, 'III' : 14, 'IV' : 18, 'V' : 21, 'X' : 18 }
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62 return break_dict
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63 elif break_file == 'Arabidopsis':
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64 break_dict = { '1' : 31 , '2' : 20, '3' : 24, '4' : 19, '5' : 27 }
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65 return break_dict
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66 else:
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67 i_file = open(break_file, 'rU')
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68 break_dict = {}
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69 reader = csv.reader(i_file, delimiter = '\t')
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70 for row in reader:
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71 chromosome = row[0].upper()
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72 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
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73 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
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74 break_count = row[1]
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75 break_dict[chromosome] = int(break_count)
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76 return break_dict
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77
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78
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79 def location_comparer(location_1, location_2):
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80 chr_loc_1 = location_1.split(':')[0]
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81 pos_loc_1 = int(location_1.split(':')[1])
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82
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83 chr_loc_2 = location_2.split(':')[0]
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84 pos_loc_2 = int(location_2.split(':')[1])
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85
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86 if chr_loc_1 == chr_loc_2:
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87 if pos_loc_1 < pos_loc_2:
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88 return -1
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89 elif pos_loc_1 == pos_loc_1:
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90 return 0
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91 elif pos_loc_1 > pos_loc_2:
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92 return 1
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93 elif chr_loc_1 < chr_loc_2:
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94 return -1
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95 elif chr_loc_1 > chr_loc_2:
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96 return 1
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97
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98 def output_vcf_info(output = None, vcf_info = None):
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99 o_file = open(output, 'wb')
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100 writer = csv.writer(o_file, delimiter = '\t')
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101
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102 writer.writerow(["#Chr\t", "Pos\t", "Alt Count\t", "Ref Count\t", "Read Depth\t", "Ratio\t"])
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103
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104 location_sorted_vcf_info_keys = sorted(vcf_info.keys(), cmp=location_comparer)
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105
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106 for location in location_sorted_vcf_info_keys:
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107 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
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108
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109 location_info = location.split(':')
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110 chromosome = location_info[0]
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111 position = location_info[1]
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112
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113 writer.writerow([chromosome, position, alt_allele_count, ref_allele_count, read_depth, ratio])
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114
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115 o_file.close()
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116
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117 def output_scatter_plots_by_location(location_plot_output = None, vcf_info = None, loess_span="", d_yaxis="", h_yaxis="", points_color="", loess_color="", standardize=None, normalized_hist_per_mb = None, normalized_hist_per_5kb = None, breaks = None, rounded_bin_size = 1000000):
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118 positions = {}
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119 current_chr = ""
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120 prev_chr = ""
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121
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122 x_label = "Location (Mb)"
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123 filtered_label = ''
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124
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125 location_sorted_vcf_info_keys = sorted(vcf_info.keys(), cmp=location_comparer)
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126
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127 break_unit = Decimal(rounded_bin_size) / Decimal(1000000)
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128 max_breaks = max(breaks.values())
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129
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130 try:
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131 r.pdf(location_plot_output, 8, 8)
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132
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133 for location in location_sorted_vcf_info_keys:
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134 current_chr = location.split(':')[0]
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135 position = location.split(':')[1]
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136
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137 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
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138
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139 if prev_chr != current_chr:
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140 if prev_chr != "":
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141 hist_dict_mb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_mb, chr = prev_chr)
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142 hist_dict_5kb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_5kb, chr = prev_chr)
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143
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144 plot_data(chr_dict = positions, hist_dict_mb = hist_dict_mb, hist_dict_5kb = hist_dict_5kb, chr = prev_chr + filtered_label, x_label = "Location (Mb)", divide_position = True, draw_secondary_grid_lines = True, loess_span=loess_span, d_yaxis=d_yaxis, h_yaxis=h_yaxis, points_color=points_color, loess_color=loess_color, breaks = breaks[prev_chr], standardize=standardize, max_breaks = max_breaks, break_unit = break_unit)
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145
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146 prev_chr = current_chr
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147 positions = {}
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148
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149 positions[position] = ratio
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150
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151 hist_dict_mb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_mb, chr = current_chr)
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152 hist_dict_5kb = get_hist_dict_by_chr(normalized_hist_per_xbase = normalized_hist_per_5kb, chr = current_chr)
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153
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154 plot_data(chr_dict = positions, hist_dict_mb = hist_dict_mb, hist_dict_5kb = hist_dict_5kb, chr = current_chr + filtered_label, x_label = "Location (Mb)", divide_position = True, draw_secondary_grid_lines = True, loess_span=loess_span, d_yaxis=d_yaxis, h_yaxis=h_yaxis, points_color=points_color, loess_color=loess_color, breaks = breaks[current_chr], standardize=standardize, max_breaks = max_breaks, break_unit = break_unit)
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155
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156 r.dev_off()
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157
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158 except Exception as inst:
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159 print inst
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160 print "There was an error creating the location plot pdf... Please try again"
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161
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162 def get_hist_dict_by_chr(normalized_hist_per_xbase = None, chr = ''):
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163 hist_dict = {}
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164
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165 for location in normalized_hist_per_xbase:
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166 chromosome = location.split(':')[0]
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167 if chromosome == chr:
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168 position = int(location.split(':')[1])
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169 hist_dict[position] = normalized_hist_per_xbase[location]
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170
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171 max_location = max(hist_dict.keys(), key=int)
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172 for i in range(1, max_location):
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173 if i not in hist_dict:
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174 hist_dict[i] = 0
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175
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176 return hist_dict
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177
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178 def plot_data(chr_dict = None, hist_dict_mb = None, hist_dict_5kb = None, chr = "", x_label = "", divide_position = False, draw_secondary_grid_lines = False, loess_span=None, d_yaxis=None, h_yaxis=None, points_color="", loess_color="", breaks = None, standardize= None, max_breaks = 1, break_unit = 1):
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179 ratios = "c("
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180 positions = "c("
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181
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182 for position in chr_dict:
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183 ratio = chr_dict[position]
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184 if divide_position:
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185 position = float(position) / 1000000.0
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186 positions = positions + str(position) + ", "
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187 ratios = ratios + str(ratio) + ", "
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188
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189 if len(ratios) == 2:
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190 ratios = ratios + ")"
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191 else:
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192 ratios = ratios[0:len(ratios) - 2] + ")"
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193
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194 if len(positions) == 2:
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195 positions = positions + ")"
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196 else:
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197 positions = positions[0:len(positions) - 2] + ")"
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198
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199 r("x <- " + positions)
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200 r("y <- " + ratios)
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201
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202 hist_mb_values = "c("
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203 for position in sorted(hist_dict_mb):
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204 hist_mb_values = hist_mb_values + str(hist_dict_mb[position]) + ", "
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205
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206 if len(hist_mb_values) == 2:
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207 hist_mb_values = hist_mb_values + ")"
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208 else:
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209 hist_mb_values = hist_mb_values[0:len(hist_mb_values) - 2] + ")"
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210
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211 hist_5kb_values = "c("
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212 for position in sorted(hist_dict_5kb):
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213 hist_5kb_values = hist_5kb_values + str(hist_dict_5kb[position]) + ", "
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214
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215 if len(hist_5kb_values) == 2:
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216 hist_5kb_values = hist_5kb_values + ")"
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217 else:
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218 hist_5kb_values = hist_5kb_values[0:len(hist_5kb_values) - 2] + ")"
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219
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220 r("xz <- " + hist_mb_values)
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221 r("yz <- " + hist_5kb_values)
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222
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223
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224 max_break_str = str(max_breaks)
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225 break_unit_str = str(Decimal(break_unit))
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226 half_break_unit_str = str(Decimal(break_unit) / Decimal(2))
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227 break_penta_unit_str = str(Decimal(break_unit) * Decimal(5))
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228
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229 if (standardize=='true'):
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230 r("plot(x, y, ,cex=0.60, xlim=c(0," + max_break_str + "), main='LG " + chr + "', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='Ratios of mapping strain alleles/total reads (at SNP positions)', pch=18, col='"+ points_color +"')")
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231 r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")
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232 r("axis(1, at=seq(0, " + max_break_str + ", by=" + break_unit_str + "), labels=FALSE, tcl=-0.5)")
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233 r("axis(1, at=seq(0, " + max_break_str + ", by=" + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
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234 r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
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235 elif (standardize=='false'):
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236 r("plot(x, y, cex=0.60, main='LG " + chr + "', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='Ratios of mapping strain alleles/total reads (at SNP positions)', pch=18, col='"+ points_color +"')")
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237 r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")
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238 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
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239 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
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240 r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
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241
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242 if draw_secondary_grid_lines:
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243 r("abline(h = seq(floor(min(y)), 1, by=0.1), v = seq(floor(min(x)), length(x), by= 1), col='gray')")
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244 else:
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245 r("grid(lty = 1, col = 'gray')")
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246
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247 if (standardize=='true'):
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248 r("barplot(xz, xlim=c(0, " + max_break_str + "), ylim = c(0, " + str(h_yaxis) + "), yaxp=c(0, " + str(h_yaxis) + ", 1), space = 0, col='darkgray', width = " + break_unit_str + ", xlab='Location (Mb)', ylab='Normalized frequency of pure parental alleles ', main='LG " + chr + "')")
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249 r("barplot(yz, space = 0, add=TRUE, width = " + half_break_unit_str + ", col=rgb(1, 0, 0, 1))")
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250 r("axis(1, hadj = 1, at=seq(0, " + max_break_str + ", by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
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251 r("axis(1, at=seq(0, " + max_break_str + ", by= " + break_penta_unit_str + "), labels=TRUE, tcl=-0.5)")
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252 r("axis(1, at=seq(0, " + max_break_str + ", by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
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253 elif (standardize=='false'):
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254 r("barplot(xz, ylim = c(0, " + str(h_yaxis) + "), yaxp=c(0, " + str(h_yaxis) + ", 1), space = 0, col='darkgray', width = 1, xlab='Location (Mb)', ylab='Normalized frequency of pure parental alleles ', main='LG " + chr + "')")
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255 r("barplot(yz, space = 0, add=TRUE, width = 0.5, col=rgb(1, 0, 0, 1))")
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256 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_unit_str + "), labels=FALSE, tcl=-0.5)")
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257 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + break_penta_unit_str + "), labels=TRUE, tcl=-0.5)")
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258 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by= " + half_break_unit_str + "), labels=FALSE, tcl=-0.25)")
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259
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260
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261
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262 def calculate_normalized_histogram_bins_per_xbase(vcf_info = None, xbase = 1000000, normalize_bins = None):
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263 normalized_histogram_bins_per_xbase = {}
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264
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265 ref_snp_count_per_xbase = get_ref_snp_count_per_xbase(vcf_info = vcf_info, xbase = xbase)
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266 #print "ref_snp_count_per_xbase: " + str(ref_snp_count_per_xbase)
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267 mean_zero_snp_count_per_chromosome = get_mean_zero_snp_count_per_chromosome(vcf_info = vcf_info, xbase = xbase)
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268 #print "mean_zero_snp_count_per_chromosome: " + str(mean_zero_snp_count_per_chromosome)
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269 zero_snp_count_per_xbase = get_zero_snp_count_per_xbase(vcf_info = vcf_info, xbase = xbase)
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270 #print "zero_snp_count_per_xbase: " + str(zero_snp_count_per_xbase)
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271
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272 for location in ref_snp_count_per_xbase:
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273 chromosome = location.split(':')[0]
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274 mean_zero_snp_count = mean_zero_snp_count_per_chromosome[chromosome]
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275 ref_snp_count = ref_snp_count_per_xbase[location]
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276
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277 zero_snp_count = 0
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278 if location in zero_snp_count_per_xbase:
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279 zero_snp_count = zero_snp_count_per_xbase[location]
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280
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281 if normalize_bins == 'true':
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282 if zero_snp_count == 0 or ref_snp_count == 0:
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283 normalized_histogram_bins_per_xbase[location] = 0
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284 elif zero_snp_count == ref_snp_count:
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285 normalized_histogram_bins_per_xbase[location] = 0
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286 else:
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287 normalized_histogram_bins_per_xbase[location] = (Decimal(zero_snp_count) / (Decimal(ref_snp_count)-Decimal(zero_snp_count))) * Decimal(mean_zero_snp_count)
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288 else:
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289 normalized_histogram_bins_per_xbase[location] = zero_snp_count
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290
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291 return normalized_histogram_bins_per_xbase
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292
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293
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294 def get_ref_snp_count_per_xbase(vcf_info = None, xbase = 1000000):
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295 ref_snps_per_xbase = {}
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296
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297 for location in vcf_info:
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298 location_info = location.split(':')
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299
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300 chromosome = location_info[0].upper()
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301 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
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302 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
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303
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304 position = location_info[1]
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305 xbase_position = (int(position) / xbase) + 1
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306
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307 location = chromosome + ":" + str(xbase_position)
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308 if location in ref_snps_per_xbase:
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309 ref_snps_per_xbase[location] = ref_snps_per_xbase[location] + 1
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310 else:
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311 ref_snps_per_xbase[location] = 1
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312
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313 return ref_snps_per_xbase
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314
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315
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316
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317 def get_mean_zero_snp_count_per_chromosome(vcf_info, xbase = 1000000):
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318 sample_snp_count_per_xbase = {}
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319
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320 for location in vcf_info:
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321 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
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322
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323 location_info = location.split(':')
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324 chromosome = location_info[0]
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325 position = location_info[1]
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326 xbase_position = (int(position) / xbase) + 1
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327 xbase_location = chromosome + ":" + str(xbase_position)
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328
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329 if int(alt_allele_count) == 0:
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330 if xbase_location in sample_snp_count_per_xbase:
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331 sample_snp_count_per_xbase[xbase_location] = sample_snp_count_per_xbase[xbase_location] + 1
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332 else:
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333 sample_snp_count_per_xbase[xbase_location] = 1
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334
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335 elif int(alt_allele_count) != 0 and xbase_location not in sample_snp_count_per_xbase:
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336 sample_snp_count_per_xbase[xbase_location] = 0
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337
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338 mean_zero_snp_count_per_chromosome = {}
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339 for location in sample_snp_count_per_xbase:
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340 chromosome = location.split(':')[0]
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341 sample_count = sample_snp_count_per_xbase[location]
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342 if chromosome in mean_zero_snp_count_per_chromosome:
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343 mean_zero_snp_count_per_chromosome[chromosome].append(sample_count)
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344 else:
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345 mean_zero_snp_count_per_chromosome[chromosome] = [sample_count]
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346
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347 for chromosome in mean_zero_snp_count_per_chromosome:
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348 summa = sum(mean_zero_snp_count_per_chromosome[chromosome])
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349 count = len(mean_zero_snp_count_per_chromosome[chromosome])
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350
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351 mean_zero_snp_count_per_chromosome[chromosome] = Decimal(summa) / Decimal(count)
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352
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353 return mean_zero_snp_count_per_chromosome
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354
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355
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356 def get_zero_snp_count_per_xbase(vcf_info = None, xbase = 1000000):
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357 zero_snp_count_per_xbase = {}
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358
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359 for location in vcf_info:
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360 alt_allele_count, ref_allele_count, read_depth, ratio = vcf_info[location]
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361
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362 location_info = location.split(':')
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363 chromosome = location_info[0]
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364 position = location_info[1]
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365 xbase_position = (int(position) / xbase) + 1
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366 xbase_location = chromosome + ":" + str(xbase_position)
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367
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|
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368 if int(alt_allele_count) == 0:
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369 if xbase_location in zero_snp_count_per_xbase:
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370 zero_snp_count_per_xbase[xbase_location] = zero_snp_count_per_xbase[xbase_location] + 1
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371 else:
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372 zero_snp_count_per_xbase[xbase_location] = 1
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373
|
|
|
374 elif int(alt_allele_count) != 0 and xbase_location not in zero_snp_count_per_xbase:
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375 zero_snp_count_per_xbase[xbase_location] = 0
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376
|
|
|
377 return zero_snp_count_per_xbase
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|
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378
|
|
|
379
|
|
|
380 def parse_vcf(sample_vcf = None):
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|
|
381 i_file = open(sample_vcf, 'rU')
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|
|
382 reader = csv.reader(i_file, delimiter = '\t', quoting = csv.QUOTE_NONE)
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|
|
383
|
|
|
384 skip_headers(reader = reader, i_file = i_file)
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|
|
385 vcf_info = {}
|
|
|
386
|
|
|
387 for row in reader:
|
|
|
388 chromosome = row[0].upper()
|
|
|
389 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
|
|
|
390 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
|
|
|
391
|
|
|
392 if chromosome != 'MTDNA':
|
|
|
393 position = row[1]
|
|
|
394 #ref_allele = row[2]
|
|
|
395 #read_depth = row[3]
|
|
|
396 #read_bases = row[4]
|
|
|
397
|
|
|
398 vcf_format_info = row[8].split(":")
|
|
|
399 vcf_allele_freq_data = row[9]
|
|
|
400
|
|
|
401 read_depth_data_index = vcf_format_info.index("DP")
|
|
|
402 read_depth = vcf_allele_freq_data.split(":")[read_depth_data_index]
|
|
|
403
|
|
|
404 ref_and_alt_counts_data_index = vcf_format_info.index("AD")
|
|
|
405 ref_and_alt_counts = vcf_allele_freq_data.split(":")[ref_and_alt_counts_data_index]
|
|
|
406 ref_allele_count = ref_and_alt_counts.split(",")[0]
|
|
|
407 alt_allele_count = ref_and_alt_counts.split(",")[1]
|
|
|
408
|
|
|
409 location = chromosome + ":" + position
|
|
|
410
|
|
|
411 if (Decimal(read_depth)!=0):
|
|
|
412 getcontext().prec = 6
|
|
|
413 ratio = Decimal(alt_allele_count) / Decimal(read_depth)
|
|
|
414
|
|
|
415 vcf_info[location] = (alt_allele_count, ref_allele_count, read_depth, ratio)
|
|
|
416
|
|
|
417 #debug line
|
|
|
418 #print chromosome, position, read_depth, ref_allele_count, alt_allele_count, ratio, id
|
|
|
419
|
|
|
420 i_file.close()
|
|
|
421
|
|
|
422 return vcf_info
|
|
|
423
|
|
|
424 def parse_read_bases(read_bases = None, alt_allele = None):
|
|
|
425 read_bases = re.sub('\$', '', read_bases)
|
|
|
426 read_bases = re.sub('\^[^\s]', '', read_bases)
|
|
|
427
|
|
|
428 ref_allele_matches = re.findall("\.|\,", read_bases)
|
|
|
429 ref_allele_count = len(ref_allele_matches)
|
|
|
430
|
|
|
431 alt_allele_matches = re.findall(alt_allele, read_bases, flags = re.IGNORECASE)
|
|
|
432 alt_allele_count = len(alt_allele_matches)
|
|
|
433
|
|
|
434 #debug line
|
|
|
435 #print read_bases, alt_allele, alt_allele_count, ref_allele_count
|
|
|
436
|
|
|
437 return ref_allele_count, alt_allele_count
|
|
|
438
|
|
|
439 if __name__ == "__main__":
|
|
|
440 main()
|
