Mercurial > repos > miller-lab > genome_diversity

comparison phylogenetic_tree.py @ 0:2c498d40ecde

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author miller-lab
date Mon, 09 Apr 2012 12:03:06 -0400
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children 248b06e86022
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-1:000000000000 0:2c498d40ecde
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
22 if len(sys.argv) < 11:
23 print >> sys.stderr, "Usage"
24 sys.exit(1)
25
26 input, p1_input, output, extra_files_path, minimum_coverage, minimum_quality, dbkey, data_source, draw_tree_options = sys.argv[1:10]
27
28 individual_metadata = sys.argv[10:]
29
30 # note: TEST THIS
31 if dbkey in ['', '?', 'None']:
32 dbkey = 'none'
33
34 p_total = Population()
35 p_total.from_tag_list(individual_metadata)
36
37
38 ################################################################################
39
40 mkdir_p(extra_files_path)
41
42 ################################################################################
43
44 def run_program(prog, args, ofh):
45 #print "args: ", ' '.join(args)
46 p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=ofh, stderr=subprocess.PIPE)
47 (stdoutdata, stderrdata) = p.communicate()
48 rc = p.returncode
49 ofh.close()
50
51 if rc != 0:
52 #print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
53 print >> sys.stderr, stderrdata
54 sys.exit(1)
55
56 ################################################################################
57
58 phylip_outfile = os.path.join(extra_files_path, 'distance_matrix.phylip')
59 newick_outfile = os.path.join(extra_files_path, 'phylogenetic_tree.newick')
60 ps_outfile = 'tree.ps'
61 pdf_outfile = os.path.join(extra_files_path, 'tree.pdf')
62
63 ################################################################################
64
65 informative_snp_file = os.path.join(extra_files_path, 'informative_snps.txt')
66 mega_distance_matrix_file = os.path.join(extra_files_path, 'mega_distance_matrix.txt')
67
68 prog = 'dist_mat'
69
70 args = []
71 args.append(prog)
72 args.append(input)
73 args.append(minimum_coverage)
74 args.append(minimum_quality)
75 args.append(dbkey)
76 args.append(data_source)
77 args.append(informative_snp_file)
78 args.append(mega_distance_matrix_file)
79
80 if p1_input == "all_individuals":
81 tags = p_total.tag_list()
82 else:
83 p1 = Population()
84 p1.from_population_file(p1_input)
85 if not p_total.is_superset(p1):
86 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
87 sys.exit(1)
88 tags = p1.tag_list()
89
90 for tag in tags:
91 args.append(tag)
92
93 fh = open(phylip_outfile, 'w')
94 run_program(None, args, fh)
95
96 ################################################################################
97
98 prog = 'quicktree'
99
100 args = []
101 args.append(prog)
102 args.append('-in')
103 args.append('m')
104 args.append('-out')
105 args.append('t')
106 args.append(phylip_outfile)
107
108 fh = open(newick_outfile, 'w')
109 run_program(None, args, fh)
110
111 ################################################################################
112
113 prog = 'draw_tree'
114
115 args = []
116 args.append(prog)
117 if draw_tree_options:
118 args.append(draw_tree_options)
119 args.append(newick_outfile)
120
121 fh = open(ps_outfile, 'w')
122 run_program(None, args, fh)
123
124 ################################################################################
125
126 prog = 'ps2pdf'
127
128 args = []
129 args.append(prog)
130 args.append('-dPDFSETTINGS=/prepress')
131 args.append(ps_outfile)
132 args.append('-')
133
134 fh = open(pdf_outfile, 'w')
135 run_program(None, args, fh)
136
137 shutil.copyfile(pdf_outfile, output)
138
139 ################################################################################
140
141 info_page = gd_composite.InfoPage()
142 info_page.set_title('Phylogenetic tree Galaxy Composite Dataset')
143
144 display_file = gd_composite.DisplayFile()
145 display_value = gd_composite.DisplayValue()
146
147 out_pdf = gd_composite.Parameter(name='tree.pdf', value='tree.pdf', display_type=display_file)
148 out_newick = gd_composite.Parameter(value='phylogenetic_tree.newick', name='phylogenetic tree (newick)', display_type=display_file)
149 out_phylip = gd_composite.Parameter(value='distance_matrix.phylip', name='Phylip distance matrix', display_type=display_file)
150 out_mega = gd_composite.Parameter(value='mega_distance_matrix.txt', name='Mega distance matrix', display_type=display_file)
151 out_snps = gd_composite.Parameter(value='informative_snps.txt', name='informative SNPs', display_type=display_file)
152
153 info_page.add_output_parameter(out_pdf)
154 info_page.add_output_parameter(out_newick)
155 info_page.add_output_parameter(out_phylip)
156 info_page.add_output_parameter(out_mega)
157 info_page.add_output_parameter(out_snps)
158
159 in_min_cov = gd_composite.Parameter(description='Minimum coverage', value=minimum_coverage, display_type=display_value)
160 in_min_qual = gd_composite.Parameter(description='Minimum quality', value=minimum_quality, display_type=display_value)
161
162 include_ref_value = 'no'
163 if dbkey != 'none':
164 include_ref_value = 'yes'
165
166 in_include_ref = gd_composite.Parameter(description='Include reference sequence', value=include_ref_value, display_type=display_value)
167
168 if data_source == '0':
169 data_source_value = 'sequence coverage'
170 elif data_source == '1':
171 data_source_value = 'estimated genotype'
172
173 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)
174
175 branch_type_value = 'square'
176 if 'd' in draw_tree_options:
177 branch_type_value = 'diagonal'
178
179 in_branch_type = gd_composite.Parameter(description='Branch type', value=branch_type_value, display_type=display_value)
180
181 branch_scale_value = 'yes'
182 if 's' in draw_tree_options:
183 branch_scale_value = 'no'
184
185 in_branch_scale = gd_composite.Parameter(description='Draw branches to scale', value=branch_scale_value, display_type=display_value)
186
187 branch_length_value = 'yes'
188 if 'b' in draw_tree_options:
189 branch_length_value = 'no'
190
191 in_branch_length = gd_composite.Parameter(description='Show branch lengths', value=branch_length_value, display_type=display_value)
192
193 tree_layout_value = 'horizontal'
194 if 'v' in draw_tree_options:
195 tree_layout_value = 'vertical'
196
197 in_tree_layout = gd_composite.Parameter(description='Tree layout', value=tree_layout_value, display_type=display_value)
198
199 info_page.add_input_parameter(in_min_cov)
200 info_page.add_input_parameter(in_min_qual)
201 info_page.add_input_parameter(in_include_ref)
202 info_page.add_input_parameter(in_data_source)
203 info_page.add_input_parameter(in_branch_type)
204 info_page.add_input_parameter(in_branch_scale)
205 info_page.add_input_parameter(in_branch_length)
206 info_page.add_input_parameter(in_tree_layout)
207
208 misc_individuals = gd_composite.Parameter(name='Individuals', value=tags, display_type=gd_composite.DisplayTagList())
209
210 info_page.add_misc(misc_individuals)
211
212
213 with open(output, 'w') as ofh:
214 print >> ofh, info_page.render()
215
216 ################################################################################
217
218 sys.exit(0)
219