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1 #!/usr/bin/env python
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2
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3 import errno
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4 import sys
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5 import os
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6 import subprocess
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7 from Population import Population
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8 import gd_composite
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9 from dpmix_plot import make_dpmix_plot
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10 from LocationFile import LocationFile
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11
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12 ################################################################################
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13
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14 def mkdir_p(path):
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15 try:
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16 os.makedirs(path)
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17 except OSError, e:
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18 if e.errno <> errno.EEXIST:
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19 raise
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20
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21 def run_program(prog, args, stdout_file=None, space_to_tab=False):
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22 #print "args: ", ' '.join(args)
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23 p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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24 (stdoutdata, stderrdata) = p.communicate()
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25 rc = p.returncode
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26
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27 if stdout_file is not None:
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28 with open(stdout_file, 'w') as ofh:
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29 lines = stdoutdata.split('\n')
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30 for line in lines:
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31 line = line.strip()
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32 if line:
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33 if space_to_tab:
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34 line = line.replace(' ', '\t')
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35 print >> ofh, line
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36
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37 if rc != 0:
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38 print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
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39 print >> sys.stderr, stderrdata
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40 sys.exit(1)
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41
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42 ################################################################################
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43
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44 if len(sys.argv) < 15:
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45 print "usage"
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46 sys.exit(1)
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47
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48 input, data_source, switch_penalty, ap1_input, ap2_input, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file = sys.argv[1:14]
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49 individual_metadata = sys.argv[14:]
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50
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51 chrom = 'all'
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52 add_logs = '0'
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53
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54 loc_path = os.path.join(galaxy_data_index_dir, heterochromatin_loc_file)
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55 location_file = LocationFile(loc_path)
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56 heterochrom_path = location_file.get_values_if_exists(dbkey)
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57 if heterochrom_path is None:
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58 heterochrom_path = '/dev/null'
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59
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60 population_list = []
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61
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62 p_total = Population()
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63 p_total.from_tag_list(individual_metadata)
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64
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65 ap1 = Population(name='Ancestral population 1')
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66 ap1.from_population_file(ap1_input)
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67 population_list.append(ap1)
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68 if not p_total.is_superset(ap1):
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69 print >> sys.stderr, 'There is an individual in ancestral population 1 that is not in the SNP table'
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70 sys.exit(1)
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71
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72 ap2 = Population(name='Ancestral population 2')
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73 ap2.from_population_file(ap2_input)
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74 population_list.append(ap2)
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75 if not p_total.is_superset(ap2):
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76 print >> sys.stderr, 'There is an individual in ancestral population 2 that is not in the SNP table'
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77 sys.exit(1)
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78
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79 p = Population(name='Potentially admixed')
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80 p.from_population_file(p_input)
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81 population_list.append(p)
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82 if not p_total.is_superset(p):
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83 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
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84 sys.exit(1)
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85
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86 mkdir_p(output2_dir)
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87
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88 ################################################################################
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89 # Create tabular file
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90 ################################################################################
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91
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92 misc_file = os.path.join(output2_dir, 'misc.txt')
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93
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94 prog = 'dpmix'
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95 args = [ prog ]
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96 args.append(input)
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97 args.append(ref_column)
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98 args.append(chrom)
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99 args.append(data_source)
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100 args.append(add_logs)
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101 args.append(switch_penalty)
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102 args.append(heterochrom_path)
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103 args.append(misc_file)
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104
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105 columns = ap1.column_list()
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106 for column in columns:
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107 args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name))
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108
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109 columns = ap2.column_list()
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110 for column in columns:
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111 args.append('{0}:2:{1}'.format(column, ap2.individual_with_column(column).name))
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112
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113 columns = p.column_list()
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114 for column in columns:
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115 args.append('{0}:0:{1}'.format(column, p.individual_with_column(column).name))
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116
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117 run_program(None, args, stdout_file=output, space_to_tab=True)
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118
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119 ################################################################################
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120 # Create pdf file
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121 ################################################################################
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122
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123 pdf_file = os.path.join(output2_dir, 'dpmix.pdf')
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124 make_dpmix_plot(dbkey, output, pdf_file, galaxy_data_index_dir)
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125
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126 ################################################################################
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127 # Create html
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128 ################################################################################
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129
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130 info_page = gd_composite.InfoPage()
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131 info_page.set_title('dpmix Galaxy Composite Dataset')
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132
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133 display_file = gd_composite.DisplayFile()
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134 display_value = gd_composite.DisplayValue()
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135
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136 out_pdf = gd_composite.Parameter(name='dpmix.pdf', value='dpmix.pdf', display_type=display_file)
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137 out_misc = gd_composite.Parameter(name='misc.txt', value='misc.txt', display_type=display_file)
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138
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139 info_page.add_output_parameter(out_pdf)
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140 info_page.add_output_parameter(out_misc)
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141
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142 if data_source == '0':
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143 data_source_value = 'sequence coverage'
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144 elif data_source == '1':
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145 data_source_value = 'estimated genotype'
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146
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147 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)
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148 in_switch_penalty = gd_composite.Parameter(description='Switch penalty', value=switch_penalty, display_type=display_value)
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149
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150 info_page.add_input_parameter(in_data_source)
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151 info_page.add_input_parameter(in_switch_penalty)
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152
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153 misc_populations = gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList())
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154
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155 info_page.add_misc(misc_populations)
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156
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157 with open(output2, 'w') as ofh:
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158 print >> ofh, info_page.render()
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159
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160 sys.exit(0)
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161
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162
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