Mercurial > repos > miller-lab > genome_diversity

annotate dpmix.py @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
parents 248b06e86022
children a631c2f6d913
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1 #!/usr/bin/env python
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3 import gd_util
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4 import sys
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5 import os
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6 from Population import Population
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7 import gd_composite
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8 from dpmix_plot import make_dpmix_plot
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9 from LocationFile import LocationFile
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10
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11 ################################################################################
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13 if len(sys.argv) != 22:
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14 print "usage"
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15 sys.exit(1)
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17 input, input_type, data_source, switch_penalty, ap1_input, ap1_name, ap2_input, ap2_name, ap3_input, ap3_name, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file, ind_arg, het_arg, add_logs = sys.argv[1:]
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18
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19 if ap3_input == '/dev/null':
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20 populations = 2
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21 else:
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22 populations = 3
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23
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24 chrom = 'all'
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25
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26 if het_arg == 'use_installed':
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27 loc_path = os.path.join(galaxy_data_index_dir, heterochromatin_loc_file)
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28 location_file = LocationFile(loc_path)
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29 heterochrom_path = location_file.get_values_if_exists(dbkey)
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30 if heterochrom_path is None:
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31 heterochrom_path = '/dev/null'
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32 elif het_arg == 'use_none':
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33 heterochrom_path = '/dev/null'
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34 else:
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35 heterochrom_path = het_arg
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37 population_list = []
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38
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39 p_total = Population()
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40 p_total.from_wrapped_dict(ind_arg)
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41
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42 ap1 = Population(name='Ancestral population 1')
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43 ap1.from_population_file(ap1_input)
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44 population_list.append(ap1)
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45 if not p_total.is_superset(ap1):
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46 gd_util.die('There is an individual in ancestral population 1 that is not in the SNP table')
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47
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48 ap2 = Population(name='Ancestral population 2')
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49 ap2.from_population_file(ap2_input)
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50 population_list.append(ap2)
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51 if not p_total.is_superset(ap2):
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52 gd_util.die('There is an individual in ancestral population 2 that is not in the SNP table')
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53
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54 if populations == 3:
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55 ap3 = Population(name='Ancestral population 3')
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56 ap3.from_population_file(ap3_input)
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57 population_list.append(ap3)
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58 if not p_total.is_superset(ap3):
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59 gd_util.die('There is an individual in ancestral population 3 that is not in the SNP table')
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60
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61 p = Population(name='Potentially admixed')
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62 p.from_population_file(p_input)
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63 population_list.append(p)
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64 if not p_total.is_superset(p):
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65 gd_util.die('There is an individual in the population that is not in the SNP table')
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66
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67 gd_util.mkdir_p(output2_dir)
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69 ################################################################################
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70 # Create tabular file
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71 ################################################################################
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72
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73 misc_file = os.path.join(output2_dir, 'summary.txt')
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75 prog = 'dpmix'
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76
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77 args = [ prog ]
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78 args.append(input)
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79 args.append(ref_column)
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80 args.append(chrom)
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81 args.append(data_source)
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82 args.append(add_logs)
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83 args.append(switch_penalty)
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84 args.append(heterochrom_path)
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85 args.append(misc_file)
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86
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87 columns = ap1.column_list()
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88 for column in columns:
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89 col = int(column)
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90 name = ap1.individual_with_column(column).name
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91 first_token = name.split()[0]
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92 if input_type == 'gd_genotype':
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93 col -= 2
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94 args.append('{0}:1:{1}'.format(col, first_token))
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95
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96 columns = ap2.column_list()
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97 for column in columns:
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98 col = int(column)
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99 name = ap2.individual_with_column(column).name
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100 first_token = name.split()[0]
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101 if input_type == 'gd_genotype':
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102 col -= 2
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103 args.append('{0}:2:{1}'.format(col, first_token))
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104
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105 if populations == 3:
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106 columns = ap3.column_list()
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107 for column in columns:
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108 col = int(column)
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109 name = ap3.individual_with_column(column).name
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110 first_token = name.split()[0]
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111 if input_type == 'gd_genotype':
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112 col -= 2
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113 args.append('{0}:3:{1}'.format(col, first_token))
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115 columns = p.column_list()
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116 for column in columns:
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117 col = int(column)
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118 name = p.individual_with_column(column).name
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119 first_token = name.split()[0]
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120 if input_type == 'gd_genotype':
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121 col -= 2
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122 args.append('{0}:0:{1}'.format(col, first_token))
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123
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124 with open(output, 'w') as fh:
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125 gd_util.run_program(prog, args, stdout=fh)
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126
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127 ################################################################################
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128 # Create pdf file
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129 ################################################################################
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130
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131 if populations == 3:
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132 state2name = {
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133 0:'heterochromatin',
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134 1:ap1_name,
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135 2:ap2_name,
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136 3:ap3_name
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137 }
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138 else:
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139 state2name = {
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140 0:'heterochromatin',
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141 1:ap1_name,
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142 2:ap2_name
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143 }
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144
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145 pdf_file = os.path.join(output2_dir, 'picture.pdf')
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146 make_dpmix_plot(dbkey, output, pdf_file, galaxy_data_index_dir, state2name=state2name, populations=populations)
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148 ################################################################################
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149 # Create html
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150 ################################################################################
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151
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152 info_page = gd_composite.InfoPage()
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153 info_page.set_title('dpmix Galaxy Composite Dataset')
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154
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155 display_file = gd_composite.DisplayFile()
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156 display_value = gd_composite.DisplayValue()
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157
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158 out_pdf = gd_composite.Parameter(name='picture.pdf', value='picture.pdf', display_type=display_file)
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159 out_misc = gd_composite.Parameter(name='summary.txt', value='summary.txt', display_type=display_file)
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160
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161 info_page.add_output_parameter(out_pdf)
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162 info_page.add_output_parameter(out_misc)
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163
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164 if data_source == '0':
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165 data_source_value = 'sequence coverage'
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166 elif data_source == '1':
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167 data_source_value = 'estimated genotype'
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168
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169 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)
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170 in_switch_penalty = gd_composite.Parameter(description='Switch penalty', value=switch_penalty, display_type=display_value)
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171
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172 info_page.add_input_parameter(in_data_source)
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173 info_page.add_input_parameter(in_switch_penalty)
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174
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175 misc_populations = gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList())
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176
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177 info_page.add_misc(misc_populations)
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178
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179 with open(output2, 'w') as ofh:
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180 print >> ofh, info_page.render()
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181
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182 sys.exit(0)
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183