annotate phylogenetic_tree.py @ 28:184d14e4270d

Update to Miller Lab devshed revision 4ede22dd5500
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 17 Jul 2013 12:46:46 -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 sys
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6 from Population import Population
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7 import gd_composite
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8
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9 ################################################################################
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11 if len(sys.argv) != 12:
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12 gd_util.die('Usage')
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14 input, output, extra_files_path, input_type, data_source_arg, minimum_coverage, minimum_quality, p1_input, dbkey, draw_tree_options, ind_arg = sys.argv[1:]
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16 if input_type == 'gd_snp':
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17 if data_source_arg == 'sequence_coverage':
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18 data_source = 0
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19 elif data_source_arg == 'estimated_genotype':
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20 data_source = 1
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21 else:
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22 gd_util.die('Unsupported data_source: {0}'.format(data_source_arg))
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23 elif input_type == 'gd_genotype':
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24 data_source = 1
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25 minimum_coverage = 0
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26 minimum_quality = 0
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27 else:
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28 gd_util.die('Unsupported input_type:: {0}'.format(input_type))
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30 # note: TEST THIS
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31 if dbkey in ['', '?', 'None']:
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32 dbkey = 'none'
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33
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34 p_total = Population()
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35 p_total.from_wrapped_dict(ind_arg)
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37 if p1_input == "all_individuals":
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38 tags = p_total.tag_list()
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39 else:
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40 p1 = Population()
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41 p1.from_population_file(p1_input)
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42 if not p_total.is_superset(p1):
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43 gd_util.die('There is an individual in the population that is not in the SNP table')
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44 tags = p1.tag_list()
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46 ################################################################################
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48 gd_util.mkdir_p(extra_files_path)
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49 phylip_outfile = os.path.join(extra_files_path, 'distance_matrix.phylip')
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50 newick_outfile = os.path.join(extra_files_path, 'phylogenetic_tree.newick')
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51 ps_outfile = 'tree.ps'
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52 pdf_outfile = os.path.join(extra_files_path, 'tree.pdf')
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53 informative_snp_file = os.path.join(extra_files_path, 'informative_snps.txt')
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54 mega_distance_matrix_file = os.path.join(extra_files_path, 'mega_distance_matrix.txt')
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56 ################################################################################
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57
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58 prog = 'dist_mat'
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59
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60 args = [ prog ]
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61 args.append(input)
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62 args.append(minimum_coverage)
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63 args.append(minimum_quality)
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64 args.append(dbkey)
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65 args.append(data_source)
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66 args.append(informative_snp_file)
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67 args.append(mega_distance_matrix_file)
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68
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69 for tag in tags:
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70 if input_type == 'gd_genotype':
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71 column, name = tag.split(':')
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72 tag = '{0}:{1}'.format(int(column) - 2, name)
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73 args.append(tag)
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74
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75 with open(phylip_outfile, 'w') as fh:
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76 gd_util.run_program(prog, args, stdout=fh)
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77
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78 ################################################################################
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79
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80 prog = 'quicktree'
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81
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82 args = [ prog ]
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83 args.append('-in')
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84 args.append('m')
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85 args.append('-out')
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86 args.append('t')
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87 args.append(phylip_outfile)
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88
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89 with open(newick_outfile, 'w') as fh:
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90 gd_util.run_program(prog, args, stdout=fh)
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91
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92 ################################################################################
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93
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94 prog = 'draw_tree'
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95
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96 args = [ prog ]
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97
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98 if draw_tree_options:
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99 args.append(draw_tree_options)
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100
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101 args.append(newick_outfile)
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102
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103 with open(ps_outfile, 'w') as fh:
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104 gd_util.run_program(prog, args, stdout=fh)
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105
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106 ################################################################################
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107
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108 prog = 'ps2pdf'
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109
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110 args = [ prog ]
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111 args.append('-dPDFSETTINGS=/prepress')
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112 args.append(ps_outfile)
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113 args.append(pdf_outfile)
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114
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115 gd_util.run_program(prog, args)
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116
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117 ################################################################################
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118
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119 info_page = gd_composite.InfoPage()
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120 info_page.set_title('Phylogenetic tree Galaxy Composite Dataset')
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121
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122 display_file = gd_composite.DisplayFile()
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123 display_value = gd_composite.DisplayValue()
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124
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125 out_pdf = gd_composite.Parameter(name='tree.pdf', value='tree.pdf', display_type=display_file)
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126 out_newick = gd_composite.Parameter(value='phylogenetic_tree.newick', name='phylogenetic tree (newick)', display_type=display_file)
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127 out_phylip = gd_composite.Parameter(value='distance_matrix.phylip', name='Phylip distance matrix', display_type=display_file)
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128 out_mega = gd_composite.Parameter(value='mega_distance_matrix.txt', name='Mega distance matrix', display_type=display_file)
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129 out_snps = gd_composite.Parameter(value='informative_snps.txt', name='informative SNPs', display_type=display_file)
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130
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131 info_page.add_output_parameter(out_pdf)
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132 info_page.add_output_parameter(out_newick)
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133 info_page.add_output_parameter(out_phylip)
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134 info_page.add_output_parameter(out_mega)
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135 info_page.add_output_parameter(out_snps)
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136
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137 in_min_cov = gd_composite.Parameter(description='Minimum coverage', value=minimum_coverage, display_type=display_value)
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138 in_min_qual = gd_composite.Parameter(description='Minimum quality', value=minimum_quality, display_type=display_value)
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139
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140 include_ref_value = 'no'
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141 if dbkey != 'none':
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142 include_ref_value = 'yes'
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143
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144 in_include_ref = gd_composite.Parameter(description='Include reference sequence', value=include_ref_value, display_type=display_value)
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145
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146 if data_source == 0:
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147 data_source_value = 'sequence coverage'
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148 elif data_source == 1:
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149 data_source_value = 'estimated genotype'
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150
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151 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)
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152
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153 branch_type_value = 'square'
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154 if 'd' in draw_tree_options:
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155 branch_type_value = 'diagonal'
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156
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157 in_branch_type = gd_composite.Parameter(description='Branch type', value=branch_type_value, display_type=display_value)
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158
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159 branch_scale_value = 'yes'
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160 if 's' in draw_tree_options:
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161 branch_scale_value = 'no'
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162
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163 in_branch_scale = gd_composite.Parameter(description='Draw branches to scale', value=branch_scale_value, display_type=display_value)
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164
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165 branch_length_value = 'yes'
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166 if 'b' in draw_tree_options:
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167 branch_length_value = 'no'
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168
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169 in_branch_length = gd_composite.Parameter(description='Show branch lengths', value=branch_length_value, display_type=display_value)
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170
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171 tree_layout_value = 'horizontal'
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172 if 'v' in draw_tree_options:
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173 tree_layout_value = 'vertical'
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174
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175 in_tree_layout = gd_composite.Parameter(description='Tree layout', value=tree_layout_value, display_type=display_value)
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176
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177 info_page.add_input_parameter(in_min_cov)
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178 info_page.add_input_parameter(in_min_qual)
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179 info_page.add_input_parameter(in_include_ref)
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180 info_page.add_input_parameter(in_data_source)
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181 info_page.add_input_parameter(in_branch_type)
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182 info_page.add_input_parameter(in_branch_scale)
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183 info_page.add_input_parameter(in_branch_length)
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184 info_page.add_input_parameter(in_tree_layout)
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185
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186 misc_individuals = gd_composite.Parameter(name='Individuals', value=tags, display_type=gd_composite.DisplayTagList())
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187
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188 info_page.add_misc(misc_individuals)
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189
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190
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191 with open(output, 'w') as ofh:
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192 print >> ofh, info_page.render()
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193
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194 ################################################################################
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195
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196 sys.exit(0)
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197