Mercurial > repos > miller-lab > genome_diversity
annotate phylogenetic_tree.py @ 25:cba0d7a63b82
workaround for gd_genotype datatype
admix shift int -> float
| author | Richard Burhans <burhans@bx.psu.edu> |
|---|---|
| date | Wed, 29 May 2013 13:49:19 -0400 |
| parents | 248b06e86022 |
| children | 8997f2ca8c7a |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
| 2 | |
| 3 import os | |
| 4 import errno | |
| 5 import sys | |
| 6 import subprocess | |
| 7 import shutil | |
| 8 from Population import Population | |
| 9 import gd_composite | |
| 10 | |
| 11 ################################################################################ | |
| 12 | |
| 13 def mkdir_p(path): | |
| 14 try: | |
| 15 os.makedirs(path) | |
| 16 except OSError, e: | |
| 17 if e.errno <> errno.EEXIST: | |
| 18 raise | |
| 19 | |
| 20 ################################################################################ | |
| 21 | |
|
24
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22 # <command interpreter="python"> |
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23 # phylogenetic_tree.py "$input" "$output" "$output.files_path" |
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24 # |
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25 # #if $input_type.choice == '0' |
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26 # "gd_snp" |
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27 # #if $input_type.data_source.choice == '0' |
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28 # "sequence_coverage" |
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29 # "$input_type.data_source.minimum_coverage" |
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30 # "$input_type.data_source.minimum_quality" |
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31 # #else if $input_type.data_source.choice == '1' |
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32 # "estimated_genotype" |
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33 # #else if $input_type.choice == '1' |
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34 # "gd_genotype" |
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35 # #end if |
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36 # |
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37 # #if $individuals.choice == '0' |
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38 # "all_individuals" |
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39 # #else if $individuals.choice == '1' |
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40 # "$individuals.p1_input" |
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41 # #end if |
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42 # |
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43 # #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0') |
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44 # "none" |
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45 # #else |
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46 # "$input.metadata.dbkey" |
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47 # #end if |
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48 # |
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49 # #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style]) |
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50 # #if $draw_tree_options == '' |
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51 # "" |
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52 # #else |
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53 # "-$draw_tree_options" |
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54 # #end if |
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55 # |
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56 # #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) |
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57 # #set $arg = '%s:%s' % ($individual_col, $individual_name) |
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58 # "$arg" |
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59 # #end for |
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60 # </command> |
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61 |
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62 ################################################################################ |
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63 |
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64 # if len(sys.argv) < 11: |
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65 # print >> sys.stderr, "Usage" |
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66 # sys.exit(1) |
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67 # |
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68 # input, p1_input, output, extra_files_path, minimum_coverage, minimum_quality, dbkey, data_source, draw_tree_options = sys.argv[1:10] |
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69 # |
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70 # individual_metadata = sys.argv[10:] |
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71 # |
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72 # # note: TEST THIS |
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73 # if dbkey in ['', '?', 'None']: |
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74 # dbkey = 'none' |
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75 # |
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76 # p_total = Population() |
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77 # p_total.from_tag_list(individual_metadata) |
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78 |
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79 if len(sys.argv) < 5: |
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80 print >> sys.stderr, 'Usage' |
| 0 | 81 sys.exit(1) |
| 82 | |
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83 input, output, extra_files_path, input_type = sys.argv[1:5] |
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84 args = sys.argv[5:] |
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85 |
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86 data_source = '1' |
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87 minimum_coverage = '0' |
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88 minimum_quality = '0' |
| 0 | 89 |
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90 if input_type == 'gd_snp': |
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91 data_source_arg = args.pop(0) |
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92 if data_source_arg == 'sequence_coverage': |
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93 data_source = '0' |
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94 minimum_coverage = args.pop(0) |
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95 minimum_quality = args.pop(0) |
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96 elif data_source_arg == 'estimated_genotype': |
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97 pass |
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98 else: |
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99 print >> sys.stderr, 'Unsupported data_source:', data_source_arg |
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100 sys.exit(1) |
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101 elif input_type == 'gd_genotype': |
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102 pass |
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103 else: |
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104 print >> sys.stderr, 'Unsupported input_type:', input_type |
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105 sys.exit(1) |
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106 |
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107 p1_input, dbkey, draw_tree_options = args[:3] |
| 0 | 108 |
| 109 # note: TEST THIS | |
| 110 if dbkey in ['', '?', 'None']: | |
| 111 dbkey = 'none' | |
| 112 | |
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113 individual_metadata = args[3:] |
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114 |
| 0 | 115 p_total = Population() |
| 116 p_total.from_tag_list(individual_metadata) | |
| 117 | |
| 118 ################################################################################ | |
| 119 | |
| 120 mkdir_p(extra_files_path) | |
| 121 | |
| 122 ################################################################################ | |
| 123 | |
| 124 def run_program(prog, args, ofh): | |
| 125 #print "args: ", ' '.join(args) | |
| 126 p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=ofh, stderr=subprocess.PIPE) | |
| 127 (stdoutdata, stderrdata) = p.communicate() | |
| 128 rc = p.returncode | |
| 129 ofh.close() | |
| 130 | |
| 131 if rc != 0: | |
| 132 #print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args)) | |
| 133 print >> sys.stderr, stderrdata | |
| 134 sys.exit(1) | |
| 135 | |
| 136 ################################################################################ | |
| 137 | |
| 138 phylip_outfile = os.path.join(extra_files_path, 'distance_matrix.phylip') | |
| 139 newick_outfile = os.path.join(extra_files_path, 'phylogenetic_tree.newick') | |
| 140 ps_outfile = 'tree.ps' | |
| 141 pdf_outfile = os.path.join(extra_files_path, 'tree.pdf') | |
| 142 | |
| 143 ################################################################################ | |
| 144 | |
| 145 informative_snp_file = os.path.join(extra_files_path, 'informative_snps.txt') | |
| 146 mega_distance_matrix_file = os.path.join(extra_files_path, 'mega_distance_matrix.txt') | |
| 147 | |
| 148 prog = 'dist_mat' | |
| 149 | |
| 150 args = [] | |
| 151 args.append(prog) | |
| 152 args.append(input) | |
| 153 args.append(minimum_coverage) | |
| 154 args.append(minimum_quality) | |
| 155 args.append(dbkey) | |
| 156 args.append(data_source) | |
| 157 args.append(informative_snp_file) | |
| 158 args.append(mega_distance_matrix_file) | |
| 159 | |
| 160 if p1_input == "all_individuals": | |
| 161 tags = p_total.tag_list() | |
| 162 else: | |
| 163 p1 = Population() | |
| 164 p1.from_population_file(p1_input) | |
| 165 if not p_total.is_superset(p1): | |
| 166 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table' | |
| 167 sys.exit(1) | |
| 168 tags = p1.tag_list() | |
| 169 | |
| 170 for tag in tags: | |
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171 if input_type == 'gd_genotype': |
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172 column, name = tag.split(':') |
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changeset
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173 tag = '{0}:{1}'.format(int(column) - 2, name) |
| 0 | 174 args.append(tag) |
| 175 | |
| 176 fh = open(phylip_outfile, 'w') | |
| 177 run_program(None, args, fh) | |
| 178 | |
| 179 ################################################################################ | |
| 180 | |
| 181 prog = 'quicktree' | |
| 182 | |
| 183 args = [] | |
| 184 args.append(prog) | |
| 185 args.append('-in') | |
| 186 args.append('m') | |
| 187 args.append('-out') | |
| 188 args.append('t') | |
| 189 args.append(phylip_outfile) | |
| 190 | |
| 191 fh = open(newick_outfile, 'w') | |
| 192 run_program(None, args, fh) | |
| 193 | |
| 194 ################################################################################ | |
| 195 | |
| 196 prog = 'draw_tree' | |
| 197 | |
| 198 args = [] | |
| 199 args.append(prog) | |
| 200 if draw_tree_options: | |
| 201 args.append(draw_tree_options) | |
| 202 args.append(newick_outfile) | |
| 203 | |
| 204 fh = open(ps_outfile, 'w') | |
| 205 run_program(None, args, fh) | |
| 206 | |
| 207 ################################################################################ | |
| 208 | |
| 209 prog = 'ps2pdf' | |
| 210 | |
| 211 args = [] | |
| 212 args.append(prog) | |
| 213 args.append('-dPDFSETTINGS=/prepress') | |
| 214 args.append(ps_outfile) | |
| 215 args.append('-') | |
| 216 | |
| 217 fh = open(pdf_outfile, 'w') | |
| 218 run_program(None, args, fh) | |
| 219 | |
| 220 shutil.copyfile(pdf_outfile, output) | |
| 221 | |
| 222 ################################################################################ | |
| 223 | |
| 224 info_page = gd_composite.InfoPage() | |
| 225 info_page.set_title('Phylogenetic tree Galaxy Composite Dataset') | |
| 226 | |
| 227 display_file = gd_composite.DisplayFile() | |
| 228 display_value = gd_composite.DisplayValue() | |
| 229 | |
| 230 out_pdf = gd_composite.Parameter(name='tree.pdf', value='tree.pdf', display_type=display_file) | |
| 231 out_newick = gd_composite.Parameter(value='phylogenetic_tree.newick', name='phylogenetic tree (newick)', display_type=display_file) | |
| 232 out_phylip = gd_composite.Parameter(value='distance_matrix.phylip', name='Phylip distance matrix', display_type=display_file) | |
| 233 out_mega = gd_composite.Parameter(value='mega_distance_matrix.txt', name='Mega distance matrix', display_type=display_file) | |
| 234 out_snps = gd_composite.Parameter(value='informative_snps.txt', name='informative SNPs', display_type=display_file) | |
| 235 | |
| 236 info_page.add_output_parameter(out_pdf) | |
| 237 info_page.add_output_parameter(out_newick) | |
| 238 info_page.add_output_parameter(out_phylip) | |
| 239 info_page.add_output_parameter(out_mega) | |
| 240 info_page.add_output_parameter(out_snps) | |
| 241 | |
| 242 in_min_cov = gd_composite.Parameter(description='Minimum coverage', value=minimum_coverage, display_type=display_value) | |
| 243 in_min_qual = gd_composite.Parameter(description='Minimum quality', value=minimum_quality, display_type=display_value) | |
| 244 | |
| 245 include_ref_value = 'no' | |
| 246 if dbkey != 'none': | |
| 247 include_ref_value = 'yes' | |
| 248 | |
| 249 in_include_ref = gd_composite.Parameter(description='Include reference sequence', value=include_ref_value, display_type=display_value) | |
| 250 | |
| 251 if data_source == '0': | |
| 252 data_source_value = 'sequence coverage' | |
| 253 elif data_source == '1': | |
| 254 data_source_value = 'estimated genotype' | |
| 255 | |
| 256 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value) | |
| 257 | |
| 258 branch_type_value = 'square' | |
| 259 if 'd' in draw_tree_options: | |
| 260 branch_type_value = 'diagonal' | |
| 261 | |
| 262 in_branch_type = gd_composite.Parameter(description='Branch type', value=branch_type_value, display_type=display_value) | |
| 263 | |
| 264 branch_scale_value = 'yes' | |
| 265 if 's' in draw_tree_options: | |
| 266 branch_scale_value = 'no' | |
| 267 | |
| 268 in_branch_scale = gd_composite.Parameter(description='Draw branches to scale', value=branch_scale_value, display_type=display_value) | |
| 269 | |
| 270 branch_length_value = 'yes' | |
| 271 if 'b' in draw_tree_options: | |
| 272 branch_length_value = 'no' | |
| 273 | |
| 274 in_branch_length = gd_composite.Parameter(description='Show branch lengths', value=branch_length_value, display_type=display_value) | |
| 275 | |
| 276 tree_layout_value = 'horizontal' | |
| 277 if 'v' in draw_tree_options: | |
| 278 tree_layout_value = 'vertical' | |
| 279 | |
| 280 in_tree_layout = gd_composite.Parameter(description='Tree layout', value=tree_layout_value, display_type=display_value) | |
| 281 | |
| 282 info_page.add_input_parameter(in_min_cov) | |
| 283 info_page.add_input_parameter(in_min_qual) | |
| 284 info_page.add_input_parameter(in_include_ref) | |
| 285 info_page.add_input_parameter(in_data_source) | |
| 286 info_page.add_input_parameter(in_branch_type) | |
| 287 info_page.add_input_parameter(in_branch_scale) | |
| 288 info_page.add_input_parameter(in_branch_length) | |
| 289 info_page.add_input_parameter(in_tree_layout) | |
| 290 | |
| 291 misc_individuals = gd_composite.Parameter(name='Individuals', value=tags, display_type=gd_composite.DisplayTagList()) | |
| 292 | |
| 293 info_page.add_misc(misc_individuals) | |
| 294 | |
| 295 | |
| 296 with open(output, 'w') as ofh: | |
| 297 print >> ofh, info_page.render() | |
| 298 | |
| 299 ################################################################################ | |
| 300 | |
| 301 sys.exit(0) | |
| 302 |