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6
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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 from rpy import *
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8
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9 def main():
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10 parser = optparse.OptionParser()
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11 parser.add_option('-s', '--snp_vcf', dest = 'snp_vcf', action = 'store', type = 'string', default = None, help = "VCF of SNPs")
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12 parser.add_option('-c', '--hist_color', dest = 'hist_color', action = 'store', type = 'string', default = "darkgray", help = "Color for 1Mb histograms")
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13 parser.add_option('-y', '--ylim', dest = 'ylim', action = 'store', type = 'int', default= 100, help = "Upper limit of Y axis")
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14 parser.add_option('-z', '--standardize', dest = 'standardize', default= 'false', help = "Standardize X-axis")
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15 parser.add_option('-e', '--ems', dest = 'ems', default= 'false', help = "Whether EMS variants should be filtered for")
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16 parser.add_option('-o', '--output', dest = 'plot_output', action = 'store', type = 'string', default = 'EMS_Variant_Density_Plot.pdf', help = "Output file name of plot")
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17 (options, args) = parser.parse_args()
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18
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19
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20 i, ii, iii, iv, v, x = parse_snp_vcf(snp_vcf = options.snp_vcf, ems=options.ems)
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21 create_histograms(plot_output = options.plot_output, hist_color=options.hist_color, ylim=options.ylim, ems=options.ems, standardize=options.standardize, i = i, ii = ii, iii = iii, iv = iv, v = v, x = x)
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22
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23 def create_histograms(plot_output = None, hist_color=None, ylim=None, ems=None, standardize=None , i = None, ii = None, iii = None, iv = None, v = None, x = None):
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24 breaks = { 'I' : 16 , 'II' : 16, 'III' : 14, 'IV' : 18, 'V' : 21, 'X' : 18 }
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25
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26 try:
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27 r.pdf(plot_output, 8, 8)
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28 if len(i) > 0:
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29 plot_data(position_list = i, chr = "I", breaks = breaks["I"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
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30 if len(ii) > 0:
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31 plot_data(position_list = ii, chr = "II", breaks = breaks["II"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
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32 if len(iii) > 0:
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33 plot_data(position_list = iii, chr = "III", breaks = breaks["III"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
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34 if len(iv) > 0:
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35 plot_data(position_list = iv, chr = "IV", breaks = breaks["IV"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
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36 if len(v) > 0:
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37 plot_data(position_list = v, chr = "V", breaks = breaks["V"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
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38 if len(x) > 0:
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39 plot_data(position_list = x, chr = "X", breaks = breaks["X"], hist_color=hist_color, ylim=ylim, ems=ems, standardize=standardize)
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40 r.dev_off()
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41 except Exception as inst:
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42 print inst
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43 print "There was an error creating the plot pdf... Please try again"
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44
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45 def parse_snp_vcf(snp_vcf = None, ems=None):
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46 i_file = open(snp_vcf, 'rU')
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47 reader = csv.reader(i_file, delimiter = '\t', quoting = csv.QUOTE_NONE)
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48
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49 skip_headers(reader = reader, i_file = i_file)
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50
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51 i_position_list = []
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52 ii_position_list = []
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53 iii_position_list = []
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54 iv_position_list = []
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55 v_position_list = []
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56 x_position_list = []
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57
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58 for row in reader:
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59 chromosome = row[0].upper()
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60 chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
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61 chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
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62
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63 position = row[1]
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64 ref_allele = row[3]
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65 alt_allele = row[4]
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66
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67 if (ems=='true'):
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68 if (ref_allele =="G" or ref_allele =="C") and (alt_allele =="A" or alt_allele =="T"):
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69 if chromosome == "I":
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70 i_position_list.append(position)
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71 elif chromosome == "II":
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72 ii_position_list.append(position)
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73 elif chromosome == "III":
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74 iii_position_list.append(position)
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75 elif chromosome == "IV":
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76 iv_position_list.append(position)
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77 elif chromosome == "V":
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78 v_position_list.append(position)
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79 elif chromosome == "X":
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80 x_position_list.append(position)
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81 elif (ems=='false'):
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82 if chromosome == "I":
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83 i_position_list.append(position)
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84 elif chromosome == "II":
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85 ii_position_list.append(position)
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86 elif chromosome == "III":
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87 iii_position_list.append(position)
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88 elif chromosome == "IV":
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89 iv_position_list.append(position)
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90 elif chromosome == "V":
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91 v_position_list.append(position)
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92 elif chromosome == "X":
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93 x_position_list.append(position)
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94
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95 return i_position_list, ii_position_list, iii_position_list, iv_position_list, v_position_list, x_position_list
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96
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97 def skip_headers(reader = None, i_file = None):
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98 # count headers
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99 comment = 0
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100 while reader.next()[0].startswith('#'):
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101 comment = comment + 1
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102
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103 # skip headers
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104 i_file.seek(0)
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105 for i in range(0, comment):
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106 reader.next()
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107
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108 def plot_data(position_list = None, chr = None, breaks = None, hist_color=None, ylim = None, ems=None, standardize=None):
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109 positions = ",".join(map(str, map(lambda x: float(x) / 1000000, position_list)))
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110 positions = "c(" + positions + ")"
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111
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112 if (standardize=='true'):
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113 r("hist(" + positions + ", xlim=c(0,21), ylim=c(0, %d "%ylim +"),col='"+ hist_color + "', breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main = 'LG " + chr + "', ylab = 'Frequency Of SNPs', xlab = 'Location (Mb)')")
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114 r("hist(" + positions + ", xlim=c(0,21), add=TRUE, ylim=c(0, %d "%ylim +"), col=rgb(1, 0, 0, 1), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main = 'Chr " + chr + "', ylab = 'Number Of SNPs', xlab = 'Location (Mb)')")
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115 r("axis(1, at=seq(0, 21, by=1), labels=FALSE, tcl=-0.5)")
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116 r("axis(1, at=seq(0, 21, by=0.5), labels=FALSE, tcl=-0.25)")
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117 elif (standardize=='false'):
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118 r("hist(" + positions + ", xlim=c(0,as.integer( ' " + str(breaks) + " ')), ylim=c(0, %d "%ylim +"),col='"+ hist_color + "', breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=1), main = 'LG " + chr + "', ylab = 'Frequency Of SNPs', xlab = 'Location (Mb)')")
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119 r("hist(" + positions + ", xlim=c(0,as.integer( ' " + str(breaks) + " ')), add=TRUE, ylim=c(0, %d "%ylim +"), col=rgb(1, 0, 0, 1), breaks = seq(0, as.integer( ' " + str(breaks) + " '), by=.5), main = 'Chr " + chr + "', ylab = 'Number Of SNPs', xlab = 'Location (Mb)')")
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120 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=1), labels=FALSE, tcl=-0.5)")
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121 r("axis(1, at=seq(0, as.integer( ' " + str(breaks) + " '), by=0.5), labels=FALSE, tcl=-0.25)")
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122
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123
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124
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125 if __name__ == "__main__":
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126 main()
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