annotate pca.py @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
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1 #!/usr/bin/env python
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2
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3 import gd_util
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4 import os
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5 import re
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6 import shutil
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7 import sys
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8 from BeautifulSoup import BeautifulSoup
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9 import gd_composite
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10
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11 ################################################################################
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12
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13 def do_ped2geno(input, output):
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14 lines = []
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15 with open(input) as fh:
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16 for line in fh:
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17 line = line.rstrip('\r\n')
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18 lines.append(line.split())
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19
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20 pair_map = {
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21 '0':{ '0':'9', '1':'9', '2':'9' },
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22 '1':{ '0':'1', '1':'2', '2':'1' },
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23 '2':{ '0':'1', '1':'1', '2':'0' }
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24 }
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25 with open(output, 'w') as ofh:
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26 for a_idx in xrange(6, len(lines[0]), 2):
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27 b_idx = a_idx + 1
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28 print >> ofh, ''.join(map(lambda line: pair_map[line[a_idx]][line[b_idx]], lines))
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29
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30 def do_map2snp(input, output):
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31 with open(output, 'w') as ofh:
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32 with open(input) as fh:
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33 for line in fh:
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34 elems = line.split()
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35 print >> ofh, ' {0} 11 0.002 2000 A T'.format(elems[1])
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36
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37 def make_ind_file(ind_file, input):
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38 pops = []
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39 name_map = []
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40 name_idx = 0
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41
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42 ofh = open(ind_file, 'w')
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43
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44 with open(input) as fh:
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45 soup = BeautifulSoup(fh)
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46 misc = soup.find('div', {'id': 'gd_misc'})
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47 populations = misc('ul')[0]
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48
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49 i = 0
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50 for entry in populations:
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51 if i % 2 == 1:
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52 population_name = entry.contents[0].encode('utf8').strip().replace(' ', '_')
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53 pops.append(population_name)
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54 individuals = entry.ol('li')
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55 for individual in individuals:
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56 individual_name = individual.string.encode('utf8').strip()
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57 name_map.append(individual_name)
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58 print >> ofh, 'ind_%s' % name_idx, 'M', population_name
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59 name_idx += 1
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60 i += 1
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61
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62 ofh.close()
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63 return pops, name_map
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64
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65 def make_par_file(par_file, geno_file, snp_file, ind_file, evec_file, eval_file):
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66 with open(par_file, 'w') as fh:
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67 print >> fh, 'genotypename: {0}'.format(geno_file)
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68 print >> fh, 'snpname: {0}'.format(snp_file)
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69 print >> fh, 'indivname: {0}'.format(ind_file)
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70 print >> fh, 'evecoutname: {0}'.format(evec_file)
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71 print >> fh, 'evaloutname: {0}'.format(eval_file)
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72 print >> fh, 'altnormstyle: NO'
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73 print >> fh, 'numoutevec: 2'
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74
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75 def do_smartpca(par_file):
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76 prog = 'smartpca'
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77
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78 args = [ prog ]
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79 args.append('-p')
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80 args.append(par_file)
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81
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82 stdoutdata, stderrdata = gd_util.run_program(prog, args)
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83
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84 stats = []
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85
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86 save_line = False
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87 for line in stdoutdata.split('\n'):
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88 if line.startswith(('## Average divergence', '## Anova statistics', '## Statistical significance')):
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89 stats.append('')
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90 save_line = True
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91 if line.strip() == '':
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92 save_line = False
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93 if save_line:
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94 stats.append(line)
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95
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96 return '\n'.join(stats[1:])
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97
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98 def do_ploteig(evec_file, population_names):
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99 prog = 'gd_ploteig'
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100
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101 args = [ prog ]
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102 args.append('-i')
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103 args.append(evec_file)
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104 args.append('-c')
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105 args.append('1:2')
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106 args.append('-p')
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107 args.append(':'.join(population_names))
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108 args.append('-x')
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109
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110 gd_util.run_program(prog, args)
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111
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112 def do_eval2pct(eval_file, explained_file):
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113 prog = 'eval2pct'
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114
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115 args = [ prog ]
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116 args.append(eval_file)
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117
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118 with open(explained_file, 'w') as fh:
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119 gd_util.run_program(prog, args, stdout=fh)
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120
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121 def do_coords2admix(coords_file):
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122 prog = 'coords2admix'
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123
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124 args = [ prog ]
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125 args.append(coords_file)
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126
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127 with open('fake', 'w') as fh:
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128 gd_util.run_program(prog, args, stdout=fh)
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129
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130 shutil.copy2('fake', coords_file)
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131
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132 ind_regex = re.compile('ind_([0-9]+)')
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133
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134 def fix_names(name_map, files):
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135 for file in files:
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136 tmp_filename = '%s.tmp' % file
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137 with open(tmp_filename, 'w') as ofh:
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138 with open(file) as fh:
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139 for line in fh:
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140 line = line.rstrip('\r\n')
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141 match = ind_regex.search(line)
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142 if match:
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143 idx = int(match.group(1))
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144 old = 'ind_%s' % idx
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145 new = name_map[idx].replace(' ', '_')
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146 line = line.replace(old, new)
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147 print >> ofh, line
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148
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149 shutil.copy2(tmp_filename, file)
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150 os.unlink(tmp_filename)
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151
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152 ################################################################################
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153
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154 if len(sys.argv) != 5:
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155 gd_util.die('Usage')
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156
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157 input, input_files_path, output, output_files_path = sys.argv[1:5]
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158 gd_util.mkdir_p(output_files_path)
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159
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160 ################################################################################
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161
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162 ped_file = os.path.join(input_files_path, 'admix.ped')
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163 geno_file = os.path.join(output_files_path, 'admix.geno')
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164 do_ped2geno(ped_file, geno_file)
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165
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166 ################################################################################
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167
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168 map_file = os.path.join(input_files_path, 'admix.map')
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169 snp_file = os.path.join(output_files_path, 'admix.snp')
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170 do_map2snp(map_file, snp_file)
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171
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172 ################################################################################
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173
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174 ind_file = os.path.join(output_files_path, 'admix.ind')
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175 population_names, name_map = make_ind_file(ind_file, input)
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177 ################################################################################
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178
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179 par_file = os.path.join(output_files_path, 'par.admix')
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180 evec_file = os.path.join(output_files_path, 'coordinates.txt')
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181 eval_file = os.path.join(output_files_path, 'admix.eval')
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182 make_par_file(par_file, geno_file, snp_file, ind_file, evec_file, eval_file)
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183
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184 ################################################################################
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185
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186 smartpca_stats = do_smartpca(par_file)
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187 fix_names(name_map, [ind_file, evec_file])
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188
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189 ################################################################################
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190
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191 do_ploteig(evec_file, population_names)
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192 plot_file = 'coordinates.txt.1:2.{0}.pdf'.format(':'.join(population_names))
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193 output_plot_file = os.path.join(output_files_path, 'PCA.pdf')
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194 shutil.copy2(plot_file, output_plot_file)
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195 os.unlink(plot_file)
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196
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197 ################################################################################
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198
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199 do_eval2pct(eval_file, os.path.join(output_files_path, 'explained.txt'))
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200 os.unlink(eval_file)
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201
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202 ################################################################################
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203
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204 do_coords2admix(evec_file)
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205
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206 ################################################################################
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207
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208 info_page = gd_composite.InfoPage()
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209 info_page.set_title('PCA Galaxy Composite Dataset')
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210
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211 display_file = gd_composite.DisplayFile()
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212 display_value = gd_composite.DisplayValue()
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213
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214 out_pdf = gd_composite.Parameter(name='PCA.pdf', value='PCA.pdf', display_type=display_file)
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215 out_evec = gd_composite.Parameter(name='coordinates.txt', value='coordinates.txt', display_type=display_file)
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216 out_explained = gd_composite.Parameter(name='explained.txt', value='explained.txt', display_type=display_file)
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217
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218 evec_prefix = 'coordinates.txt.1:2.{0}'.format(':'.join(population_names))
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219 ps_file = '{0}.ps'.format(evec_prefix)
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220 xtxt_file = '{0}.xtxt'.format(evec_prefix)
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221
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222 os.unlink(os.path.join(output_files_path, ps_file))
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223 os.unlink(os.path.join(output_files_path, xtxt_file))
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224
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225 info_page.add_output_parameter(out_pdf)
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226 info_page.add_output_parameter(out_evec)
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227 info_page.add_output_parameter(out_explained)
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228
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229 in_admix = gd_composite.Parameter(name='par.admix', value='par.admix', display_type=display_file)
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230 in_geno = gd_composite.Parameter(name='admix.geno', value='admix.geno', display_type=display_file)
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231 in_snp = gd_composite.Parameter(name='admix.snp', value='admix.snp', display_type=display_file)
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232 in_ind = gd_composite.Parameter(name='admix.ind', value='admix.ind', display_type=display_file)
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233
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234 info_page.add_input_parameter(in_admix)
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235 info_page.add_input_parameter(in_geno)
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236 info_page.add_input_parameter(in_snp)
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237 info_page.add_input_parameter(in_ind)
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238
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239 misc_stats = gd_composite.Parameter(description='Stats<p/><pre>\n{0}\n</pre>'.format(smartpca_stats), display_type=display_value)
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240
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241 info_page.add_misc(misc_stats)
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242
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243 with open (output, 'w') as ofh:
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244 print >> ofh, info_page.render()
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245
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246 sys.exit(0)
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247