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0
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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 from decimal import *
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9 from rpy import *
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10
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11 def main():
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12 csv.field_size_limit(1000000000)
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13
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14 parser = optparse.OptionParser()
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15 parser.add_option('-p', '--sample_pileup', dest = 'sample_pileup', action = 'store', type = 'string', default = None, help = "Sample pileup from mpileup")
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16 parser.add_option('-v', '--haw_vcf', dest = 'haw_vcf', action = 'store', type = 'string', default = None, help = "vcf file of Hawaiian SNPs")
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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 = 500, help = "y-axis upper limit for dot 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= 'false', help = "Standardize X-axis")
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23
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24 parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name")
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25 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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26
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27 #For plotting with map units on the X-axis instead of physical distance
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28 #parser.add_option('-u', '--mpu_plot_output', dest = 'mpu_plot_output', action = 'store', type = 'string', default = None, help = "Output file name of SNP plots by map unit location")
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29 (options, args) = parser.parse_args()
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30
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31 haw_snps = build_haw_snp_dictionary(haw_vcf = options.haw_vcf)
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32 pileup_info = parse_pileup(sample_pileup = options.sample_pileup, haw_snps = haw_snps)
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33 output_pileup_info(output = options.output, pileup_info = pileup_info)
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34
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35 #output plot with all ratios
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36 output_scatter_plots_by_location(location_plot_output = options.location_plot_output, pileup_info = pileup_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)
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37
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38 #For plotting with map units on the X-axis instead of physical distance)
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39 #output_scatter_plots_by_mapping_units(mpu_plot_output = options.mpu_plot_output, pileup_info = pileup_info)
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40
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41 def skip_headers(reader = None, i_file = None):
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42 # count headers
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43 comment = 0
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44 while reader.next()[0].startswith('#'):
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45 comment = comment + 1
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46
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47 # skip headers
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48 i_file.seek(0)
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49 for i in range(0, comment):
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50 reader.next()
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51
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52 def location_comparer(location_1, location_2):
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53 chr_loc_1 = location_1.split(':')[0]
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54 pos_loc_1 = int(location_1.split(':')[1])
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55
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56 chr_loc_2 = location_2.split(':')[0]
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57 pos_loc_2 = int(location_2.split(':')[1])
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58
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59 if chr_loc_1 == chr_loc_2:
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60 if pos_loc_1 < pos_loc_2:
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61 return -1
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62 elif pos_loc_1 == pos_loc_1:
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63 return 0
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64 elif pos_loc_1 > pos_loc_2:
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65 return 1
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66 elif chr_loc_1 < chr_loc_2:
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67 return -1
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68 elif chr_loc_1 > chr_loc_2:
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69 return 1
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70
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71 def output_pileup_info(output = None, pileup_info = None):
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72 o_file = open(output, 'wb')
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73 writer = csv.writer(o_file, delimiter = '\t')
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74
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75 writer.writerow(["#Chr\t", "Pos\t", "ID\t", "Alt Count\t", "Ref Count\t", "Read Depth\t", "Ratio\t", "Mapping Unit"])
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76
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77 location_sorted_pileup_info_keys = sorted(pileup_info.keys(), cmp=location_comparer)
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78
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79 for location in location_sorted_pileup_info_keys:
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80 alt_allele_count, ref_allele_count, read_depth, ratio, haw_snp_id, mapping_unit = pileup_info[location]
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81
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82 location_info = location.split(':')
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83 chromosome = location_info[0]
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84 position = location_info[1]
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85
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86 writer.writerow([chromosome, position, haw_snp_id, alt_allele_count, ref_allele_count, read_depth, ratio, mapping_unit])
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87
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88 o_file.close()
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89
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90 def output_scatter_plots_by_location(location_plot_output = None, pileup_info = None, loess_span="", d_yaxis="", h_yaxis="", points_color="", loess_color="", standardize=None):
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91 i = {}
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92 ii = {}
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93 iii = {}
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94 iv = {}
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95 v = {}
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96 x = {}
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97
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98 breaks = { 'I' : 16 , 'II' : 16, 'III' : 14, 'IV' : 18, 'V' : 21, 'X' : 18 }
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99
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100 for location in pileup_info:
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101 chromosome = location.split(':')[0]
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102 position = location.split(':')[1]
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103
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104 alt_allele_count, ref_allele_count, read_depth, ratio, haw_snp_id, mapping_unit = pileup_info[location]
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105
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106 if chromosome == "I":
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107 i[position] = ratio
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108 elif chromosome == "II":
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109 ii[position] = ratio
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110 elif chromosome == "III":
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111 iii[position] = ratio
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112 elif chromosome == "IV":
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113 iv[position] = ratio
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114 elif chromosome == "V":
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115 v[position] = ratio
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116 elif chromosome == "X":
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117 x[position] = ratio
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118
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119 x_label = "Location (Mb)"
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120 filtered_label = ''
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121
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122
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123 try:
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124 r.pdf(location_plot_output, 8, 8)
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125 if i:
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126 plot_data(chr_dict = i, chr = "I" + 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["I"], standardize=standardize)
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127 if ii:
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128 plot_data(chr_dict = ii, chr = "II" + 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["II"], standardize=standardize)
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129 if iii:
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130 plot_data(chr_dict = iii, chr = "III" + 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["III"], standardize=standardize)
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131 if iv:
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132 plot_data(chr_dict = iv, chr = "IV" + 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["IV"], standardize=standardize)
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133 if v:
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134 plot_data(chr_dict = v, chr = "V" + 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["V"], standardize=standardize)
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135 if x:
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136 plot_data(chr_dict = x, chr = "X" + 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["X"], standardize=standardize)
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137
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138 r.dev_off()
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139 except Exception as inst:
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140 print inst
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141 print "There was an error creating the location plot pdf... Please try again"
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142
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143 def output_scatter_plots_by_mapping_units(mpu_plot_output = None, pileup_info = None):
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144 i = {}
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145 ii = {}
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146 iii = {}
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147 iv = {}
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148 v = {}
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149 x = {}
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150
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151 for location in pileup_info:
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152 chromosome = location.split(':')[0]
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153 position = location.split(':')[1]
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154
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155 alt_allele_count, ref_allele_count, read_depth, ratio, haw_snp_id, mapping_unit = pileup_info[location]
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156
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157 if chromosome == "I":
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158 i[mapping_unit] = ratio
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159 elif chromosome == "II":
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160 ii[mapping_unit] = ratio
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161 elif chromosome == "III":
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162 iii[mapping_unit] = ratio
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163 elif chromosome == "IV":
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164 iv[mapping_unit] = ratio
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165 elif chromosome == "V":
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166 v[mapping_unit] = ratio
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167 elif chromosome == "X":
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168 x[mapping_unit] = ratio
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169
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170 x_label = "Map Units"
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171
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172 try:
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173 r.pdf(mpu_plot_output, 8, 8)
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174 plot_data(chr_dict = i, chr = "I", x_label = "Map Units")
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175 plot_data(chr_dict = ii, chr = "II", x_label = "Map Units")
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176 plot_data(chr_dict = iii, chr = "III", x_label = "Map Units")
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177 plot_data(chr_dict = iv, chr = "IV", x_label = "Map Units")
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178 plot_data(chr_dict = v, chr = "V", x_label = "Map Units")
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179 plot_data(chr_dict = x, chr = "X", x_label = "Map Units")
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180 r.dev_off()
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181 except Exception as inst:
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182 print inst
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183 print "There was an error creating the map unit plot pdf... Please try again"
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184
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185
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186 def plot_data(chr_dict = 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):
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187 ratios = "c("
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188 positions = "c("
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189 z_ratios = "c("
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190 z_positions = "c("
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191
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192 for position in chr_dict:
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193 ratio = chr_dict[position]
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194 if divide_position:
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195 position = float(position) / 1000000.0
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196 positions = positions + str(position) + ", "
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197 ratios = ratios + str(ratio) + ", "
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198 if ratio == 0:
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199 if divide_position:
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200 z_position = float(position) / 1000000.0
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201 z_positions = z_positions + str(position) + ", "
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202 z_ratios = z_ratios + str(ratio) + ", "
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203
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204
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205 if len(ratios) == 2:
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206 ratios = ratios + ")"
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207 else:
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208 ratios = ratios[0:len(ratios) - 2] + ")"
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209
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210 if len(z_ratios) == 2:
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211 z_ratios = z_ratios + ")"
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212 else:
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213 z_ratios = z_ratios[0:len(z_ratios) - 2] + ")"
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214
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215
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216 if len(positions) == 2:
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217 positions = positions + ")"
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218 else:
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219 positions = positions[0:len(positions) - 2] + ")"
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220
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221 if len(z_positions) == 2:
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222 z_positions = z_positions + ")"
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223 else:
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224 z_positions = z_positions[0:len(z_positions) - 2] + ")"
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225
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226 r("x <- " + positions)
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227 r("y <- " + ratios)
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228
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229 r("xz <- " + z_positions)
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230 r("yz <- " + z_ratios)
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231
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232 if (standardize=='true'):
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233 r("plot(x, y, cex=0.60, xlim=c(0,21), main='LG " + chr + "', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='HA Ratio [Hawaiian Reads / Total Read Depth]', pch=18, col='"+ points_color +"')")
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234 r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")
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235 r("axis(1, at=seq(0, 21, by=1), labels=FALSE, tcl=-0.5)")
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236 r("axis(1, at=seq(0, 21, by=0.5), labels=FALSE, tcl=-0.25)")
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237 r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
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238 elif (standardize=='false'):
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239 r("plot(x, y, cex=0.60, main='LG " + chr + "', xlab= '" + x_label + "', ylim = c(0, %f " %d_yaxis + "), ylab='HA Ratio [Hawaiian Reads / Total Read Depth]', pch=18, col='"+ points_color +"')")
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240 r("lines(loess.smooth(x, y, span = %f "%loess_span + "), lwd=5, col='"+ loess_color +"')")
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241 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=1), labels=FALSE, tcl=-0.5)")
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242 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=0.5), labels=FALSE, tcl=-0.25)")
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243 r("axis(2, at=seq(floor(min(y)), 1, by=0.1), labels=FALSE, tcl=-0.2)")
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244
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245
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246 if draw_secondary_grid_lines:
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247 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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248 else:
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249 r("grid(lty = 1, col = 'gray')")
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250
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251 if (standardize=='true'):
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252 r("hist(xz, col='darkgray', xlim=c(0,21), xlab='Location (Mb)', ylab='Frequency SNP Positions Where HA Ratio=0 ', ylim=c(0, %f " %h_yaxis + "), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main='LG " + chr + "')")
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253 r("hist(xz, add=TRUE, col=rgb(1, 0, 0, 1), xlim=c(0,21), xlab='Location (Mb)', ylab='Frequency SNP Positions Where HA Ratio=0 ', ylim=c(0, %f " %h_yaxis + "), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main='Chr " + chr + "')")
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254 r("axis(1, at=seq(0, 21, by=1), labels=FALSE, tcl=-0.5)")
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255 r("axis(1, at=seq(0, 21, by=0.5), labels=FALSE, tcl=-0.25)")
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256 elif (standardize=='false'):
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257 r("hist(xz, col='darkgray', xlab='Location (Mb)', ylab='Frequency SNP Positions Where HA Ratio=0 ', ylim=c(0, %f " %h_yaxis + "), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main='LG " + chr + "')")
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258 r("hist(xz, add=TRUE, col=rgb(1, 0, 0, 1), xlab='Location (Mb)', ylab='Frequency SNP Positions Where HA Ratio=0 ', ylim=c(0, %f " %h_yaxis + "), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main='Chr " + chr + "')")
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259 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=1), labels=FALSE, tcl=-0.5)")
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260 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=0.5), labels=FALSE, tcl=-0.25)")
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261
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262
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263 def build_haw_snp_dictionary(haw_vcf = None):
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264 haw_snps = {}
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265
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266 i_file = open(haw_vcf, 'rU')
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267 reader = csv.reader(i_file, delimiter = '\t')
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268
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269 skip_headers(reader = reader, i_file = i_file)
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270
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271 for row in reader:
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272 #print row
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273 chromosome = row[0].upper()
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274 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
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275 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
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276
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277 position = row[1]
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278 haw_snp_id = row[2]
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279 ref_allele = row[3]
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280 alt_allele = row[4]
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281 info = row[7]
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282
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283 mapping_unit = info.replace("MPU=", "")
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284
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285 location = chromosome + ":" + position
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286 haw_snps[location] = (alt_allele, haw_snp_id, mapping_unit)
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287
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288 i_file.close()
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289
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290 return haw_snps
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291
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292 def parse_pileup(sample_pileup = None, haw_snps = None):
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293 i_file = open(sample_pileup, 'rU')
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294 reader = csv.reader(i_file, delimiter = '\t', quoting = csv.QUOTE_NONE)
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295
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296 pileup_info = {}
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297
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298 for row in reader:
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299 chromosome = row[0].upper()
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300 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
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301 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
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302
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303 position = row[1]
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304 ref_allele = row[2]
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305 read_depth = row[3]
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306 read_bases = row[4]
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307
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308 location = chromosome + ":" + position
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309 if location in haw_snps:
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310 alt_allele, haw_snp_id, mapping_unit = haw_snps[location]
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311 ref_allele_count, alt_allele_count = parse_read_bases(read_bases = read_bases, alt_allele = alt_allele)
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312
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313 getcontext().prec = 6
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314 ratio = Decimal(alt_allele_count) / Decimal(read_depth)
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315
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316 pileup_info[location] = (alt_allele_count, ref_allele_count, read_depth, ratio, haw_snp_id, mapping_unit)
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317
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318 #debug line
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319 #print chromosome, position, read_depth, ref_allele_count, alt_allele_count, ratio, id
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320
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321 i_file.close()
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322
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323 return pileup_info
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324
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325 def parse_read_bases(read_bases = None, alt_allele = None):
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326 read_bases = re.sub('\$', '', read_bases)
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327 read_bases = re.sub('\^[^\s]', '', read_bases)
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328
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329 ref_allele_matches = re.findall("\.|\,", read_bases)
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330 ref_allele_count = len(ref_allele_matches)
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331
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332 alt_allele_matches = re.findall(alt_allele, read_bases, flags = re.IGNORECASE)
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333 alt_allele_count = len(alt_allele_matches)
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334
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335 #debug line
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336 #print read_bases, alt_allele, alt_allele_count, ref_allele_count
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337
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338 return ref_allele_count, alt_allele_count
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339
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340 if __name__ == "__main__":
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341 main()
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