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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 os
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5 import shutil
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6 import subprocess
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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 run_admixture(ped_file, populations):
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14 prog = 'admixture'
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15
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16 args = []
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17 args.append(prog)
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18 args.append(input_ped_file)
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19 args.append(populations)
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20
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21 #print "args:", ' '.join(args)
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22 ofh = open('/dev/null', 'w')
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23 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=ofh, stderr=sys.stderr)
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24 rc = p.wait()
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25 ofh.close()
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26
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27 def run_r(input_file, output_file, populations):
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28 prog = 'R'
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29
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30 args = []
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31 args.append(prog)
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32 args.append('--vanilla')
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33 args.append('--quiet')
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34 args.append('--args')
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35 args.append(input_file)
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36 args.append(output_file)
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37 args.append(populations)
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38
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39 _realpath = os.path.realpath(__file__)
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40 _script_dir = os.path.dirname(_realpath)
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41 r_script_file = os.path.join(_script_dir, 'population_structure.r')
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42
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43 ifh = open(r_script_file)
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44 ofh = open('/dev/null', 'w')
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45 p = subprocess.Popen(args, bufsize=-1, stdin=ifh, stdout=ofh, stderr=None)
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46 rc = p.wait()
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47 ifh.close()
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48 ofh.close()
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49
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50 def mkdir_p(path):
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51 try:
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52 os.makedirs(path)
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53 except OSError, e:
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54 if e.errno <> errno.EEXIST:
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55 raise
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56
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57 def get_populations(input):
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58 pops = []
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59 pop_names = {}
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60
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61 with open(input) as fh:
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62 soup = BeautifulSoup(fh)
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63 misc = soup.find('div', {'id': 'gd_misc'})
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64
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65 return 'Populations\n{0}'.format(misc('ul')[0])
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66
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67 ################################################################################
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68
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69 if len(sys.argv) != 6:
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70 print >> sys.stderr, "Usage"
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71 sys.exit(1)
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72
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73 input_html_file, input_ped_file, output_file, extra_files_path, populations = sys.argv[1:6]
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74 populations_html = get_populations(input_html_file)
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75
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76 run_admixture(input_ped_file, populations)
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77
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78 ped_base = os.path.basename(input_ped_file)
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79 if ped_base.endswith('.ped'):
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80 ped_base = ped_base[:-4]
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81
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82 p_file = '%s.%s.P' % (ped_base, populations)
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83 q_file = '%s.%s.Q' % (ped_base, populations)
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84
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85 mkdir_p(extra_files_path)
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86 numeric_output_file = os.path.join(extra_files_path, 'numeric.txt')
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87 shutil.copy2(q_file, numeric_output_file)
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88 os.remove(p_file)
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89 os.remove(q_file)
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90
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91 graphical_output_file = os.path.join(extra_files_path, 'graphical.pdf')
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92 run_r(numeric_output_file, graphical_output_file, populations)
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93
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94 ################################################################################
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95
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96 info_page = gd_composite.InfoPage()
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97 info_page.set_title('Population structure Galaxy Composite Dataset')
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98
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99 display_file = gd_composite.DisplayFile()
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100 display_value = gd_composite.DisplayValue()
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101
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102 out_pdf = gd_composite.Parameter(name='graphical.pdf', value='graphical.pdf', display_type=display_file)
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103 out_txt = gd_composite.Parameter(name='numeric.txt', value='numeric.txt', display_type=display_file)
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104
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105 info_page.add_output_parameter(out_pdf)
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106 info_page.add_output_parameter(out_txt)
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107
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108 in_pops = gd_composite.Parameter(description='Number of populations', value=populations, display_type=display_value)
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109
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110 info_page.add_input_parameter(in_pops)
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111
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112 misc_pops = gd_composite.Parameter(description=populations_html, display_type=display_value)
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113
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114 info_page.add_misc(misc_pops)
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115
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116
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117 with open (output_file, 'w') as ofh:
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118 print >> ofh, info_page.render()
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119
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120
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121 sys.exit(0)
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