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annotate dpmix.py @ 35:ea52b23f1141

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Bug fixes for Draw variants, Phylip, and gd_d_tools
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 13:46:10 -0500
parents 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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11 def load_and_check_pop(name, file, total_pop):
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12 p = Population(name=name)
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13 p.from_population_file(file)
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14 if not total_pop.is_superset(p):
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15 gd_util.die('There is an individual in {0} that is not in the SNP table'.format(name))
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16 return p
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17
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18 def append_pop_tags(the_list, p, input_type, number):
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19 for tag in p.tag_list():
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20 column, name = tag.split(':')
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21 if input_type == 'gd_genotype':
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22 column = int(column) - 2
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23 the_list.append('{0}:{1}:{2}'.format(column, number, name))
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24
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25 ################################################################################
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27 if len(sys.argv) != 22:
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28 print "usage"
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29 sys.exit(1)
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31 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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32
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33 if ap1_input == '/dev/null':
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34 use_reference = True
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35 else:
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36 use_reference = False
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37
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38 if ap3_input == '/dev/null':
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39 populations = 2
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40 else:
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41 populations = 3
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42
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43 chrom = 'all'
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44
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45 if het_arg == 'use_installed':
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46 loc_path = os.path.join(galaxy_data_index_dir, heterochromatin_loc_file)
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47 location_file = LocationFile(loc_path)
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48 heterochrom_path = location_file.get_values_if_exists(dbkey)
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49 if heterochrom_path is None:
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50 heterochrom_path = '/dev/null'
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51 elif het_arg == 'use_none':
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52 heterochrom_path = '/dev/null'
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53 else:
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54 heterochrom_path = het_arg
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55
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56 population_list = []
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57
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58 p_total = Population()
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59 p_total.from_wrapped_dict(ind_arg)
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61 if not use_reference:
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62 ap1 = load_and_check_pop('Ancestral population 1', ap1_input, p_total)
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63 population_list.append(ap1)
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65 ap2 = load_and_check_pop('Ancestral population 2', ap2_input, p_total)
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66 population_list.append(ap2)
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67
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68 if populations == 3:
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69 ap3 = load_and_check_pop('Ancestral population 3', ap3_input, p_total)
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70 population_list.append(ap3)
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72 p = load_and_check_pop('Potentially admixed', p_input, p_total)
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73 population_list.append(p)
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75 gd_util.mkdir_p(output2_dir)
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76
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77 ################################################################################
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78 # Create tabular file
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79 ################################################################################
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80
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81 misc_file = os.path.join(output2_dir, 'summary.txt')
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82
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83 prog = 'dpmix'
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84
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85 args = [ prog ]
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86 args.append(input)
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87 args.append(ref_column)
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88 args.append(chrom)
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89 args.append(data_source)
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90 args.append(add_logs)
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91 args.append(switch_penalty)
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92 args.append(heterochrom_path)
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93 args.append(misc_file)
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94
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95 if use_reference:
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96 args.append('0:1:reference')
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97 else:
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98 append_pop_tags(args, ap1, input_type, 1)
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100 append_pop_tags(args, ap2, input_type, 2)
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101
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102 if populations == 3:
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103 append_pop_tags(args, ap3, input_type, 3)
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105 append_pop_tags(args, p, input_type, 0)
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106
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107 with open(output, 'w') as fh:
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108 gd_util.run_program(prog, args, stdout=fh)
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110 ################################################################################
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111 # Create pdf file
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112 ################################################################################
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113
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114 if populations == 3:
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115 state2name = {
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116 0:'heterochromatin',
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117 1:ap1_name,
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118 2:ap2_name,
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119 3:ap3_name
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120 }
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121 else:
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122 state2name = {
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123 0:'heterochromatin',
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124 1:ap1_name,
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125 2:ap2_name
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126 }
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127
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128 pdf_file = os.path.join(output2_dir, 'picture.pdf')
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129 make_dpmix_plot(dbkey, output, pdf_file, galaxy_data_index_dir, state2name=state2name, populations=populations)
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130
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131 ################################################################################
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132 # Create html
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133 ################################################################################
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134
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135 info_page = gd_composite.InfoPage()
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136 info_page.set_title('dpmix Galaxy Composite Dataset')
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137
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138 display_file = gd_composite.DisplayFile()
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139 display_value = gd_composite.DisplayValue()
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140
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141 out_pdf = gd_composite.Parameter(name='picture.pdf', value='picture.pdf', display_type=display_file)
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142 out_misc = gd_composite.Parameter(name='summary.txt', value='summary.txt', display_type=display_file)
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143
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144 info_page.add_output_parameter(out_pdf)
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145 info_page.add_output_parameter(out_misc)
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146
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147 if data_source == '0':
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148 data_source_value = 'sequence coverage'
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149 elif data_source == '1':
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150 data_source_value = 'estimated genotype'
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151
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152 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)
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153 in_switch_penalty = gd_composite.Parameter(description='Switch penalty', value=switch_penalty, display_type=display_value)
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154
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155 info_page.add_input_parameter(in_data_source)
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156 info_page.add_input_parameter(in_switch_penalty)
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157
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158 misc_populations = gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList())
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159
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160 info_page.add_misc(misc_populations)
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161
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162 with open(output2, 'w') as ofh:
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163 print >> ofh, info_page.render()
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164
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165 sys.exit(0)
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166