Mercurial > repos > miller-lab > genome_diversity

comparison pca.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 errno
4 import os
5 import shutil
6 import subprocess
7 import sys
8 from BeautifulSoup import BeautifulSoup
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 def run_program(prog, args, stdout_file=None):
23 #print "args: ", ' '.join(args)
24 p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
25 (stdoutdata, stderrdata) = p.communicate()
26 rc = p.returncode
27
28 if stdout_file is not None:
29 with open(stdout_file, 'w') as ofh:
30 print >> ofh, stdoutdata
31
32 if rc != 0:
33 print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
34 print >> sys.stderr, stderrdata
35 sys.exit(1)
36
37 ################################################################################
38
39 def do_ped2geno(input, output):
40 lines = []
41 with open(input) as fh:
42 for line in fh:
43 line = line.rstrip('\r\n')
44 lines.append(line.split())
45
46 pair_map = {
47 '0':{ '0':'9', '1':'9', '2':'9' },
48 '1':{ '0':'1', '1':'2', '2':'1' },
49 '2':{ '0':'1', '1':'1', '2':'0' }
50 }
51 with open(output, 'w') as ofh:
52 for a_idx in xrange(6, len(lines[0]), 2):
53 b_idx = a_idx + 1
54 print >> ofh, ''.join(map(lambda line: pair_map[line[a_idx]][line[b_idx]], lines))
55
56 def do_map2snp(input, output):
57 with open(output, 'w') as ofh:
58 with open(input) as fh:
59 for line in fh:
60 elems = line.split()
61 print >> ofh, ' {0} 11 0.002 2000 A T'.format(elems[1])
62
63 def make_ind_file(ind_file, input):
64 pops = []
65
66 ofh = open(ind_file, 'w')
67
68 with open(input) as fh:
69 soup = BeautifulSoup(fh)
70 misc = soup.find('div', {'id': 'gd_misc'})
71 populations = misc('ul')[0]
72
73 i = 0
74 for entry in populations:
75 if i % 2 == 1:
76 population_name = entry.contents[0].encode('utf8').strip().replace(' ', '_')
77 pops.append(population_name)
78 individuals = entry.ol('li')
79 for individual in individuals:
80 individual_name = individual.string.encode('utf8').strip()
81 print >> ofh, individual_name, 'M', population_name
82 i += 1
83
84 ofh.close()
85 return pops
86
87 def make_par_file(par_file, geno_file, snp_file, ind_file, evec_file, eval_file):
88 with open(par_file, 'w') as fh:
89 print >> fh, 'genotypename: {0}'.format(geno_file)
90 print >> fh, 'snpname: {0}'.format(snp_file)
91 print >> fh, 'indivname: {0}'.format(ind_file)
92 print >> fh, 'evecoutname: {0}'.format(evec_file)
93 print >> fh, 'evaloutname: {0}'.format(eval_file)
94 print >> fh, 'altnormstyle: NO'
95 print >> fh, 'numoutevec: 2'
96
97 def do_smartpca(par_file):
98 prog = 'smartpca'
99
100 args = [ prog ]
101 args.append('-p')
102 args.append(par_file)
103
104 #print "args: ", ' '.join(args)
105 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=subprocess.PIPE, stderr=sys.stderr)
106 (stdoutdata, stderrdata) = p.communicate()
107 rc = p.returncode
108
109 if rc != 0:
110 print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
111 print >> sys.stderr, stderrdata
112 sys.exit(1)
113
114 stats = []
115
116 save_line = False
117 for line in stdoutdata.split('\n'):
118 if line.startswith(('## Average divergence', '## Anova statistics', '## Statistical significance')):
119 stats.append('')
120 save_line = True
121 if line.strip() == '':
122 save_line = False
123 if save_line:
124 stats.append(line)
125
126 return '\n'.join(stats[1:])
127
128 def do_ploteig(evec_file, population_names):
129 prog = 'gd_ploteig'
130
131 args = [ prog ]
132 args.append('-i')
133 args.append(evec_file)
134 args.append('-c')
135 args.append('1:2')
136 args.append('-p')
137 args.append(':'.join(population_names))
138 args.append('-x')
139
140 run_program(None, args)
141
142 def do_eval2pct(eval_file, explained_file):
143 prog = 'eval2pct'
144
145 args = [ prog ]
146 args.append(eval_file)
147
148 with open(explained_file, 'w') as ofh:
149 #print "args:", ' '.join(args)
150 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=ofh, stderr=subprocess.PIPE)
151 (stdoutdata, stderrdata) = p.communicate()
152 rc = p.returncode
153
154 if rc != 0:
155 print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
156 print >> sys.stderr, stderrdata
157 sys.exit(1)
158
159 def do_coords2admix(coords_file):
160 prog = 'coords2admix'
161
162 args = [ prog ]
163 args.append(coords_file)
164
165 with open('fake', 'w') as ofh:
166 #print "args:", ' '.join(args)
167 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=ofh, stderr=subprocess.PIPE)
168 (stdoutdata, stderrdata) = p.communicate()
169 rc = p.returncode
170
171 if rc != 0:
172 print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
173 print >> sys.stderr, stderrdata
174 sys.exit(1)
175
176 shutil.copy2('fake', coords_file)
177
178 ################################################################################
179
180 if len(sys.argv) != 5:
181 print "usage"
182 sys.exit(1)
183
184 input, input_files_path, output, output_files_path = sys.argv[1:5]
185
186 mkdir_p(output_files_path)
187
188 ped_file = os.path.join(input_files_path, 'admix.ped')
189 geno_file = os.path.join(output_files_path, 'admix.geno')
190 do_ped2geno(ped_file, geno_file)
191
192 map_file = os.path.join(input_files_path, 'admix.map')
193 snp_file = os.path.join(output_files_path, 'admix.snp')
194 do_map2snp(map_file, snp_file)
195
196 ind_file = os.path.join(output_files_path, 'admix.ind')
197 population_names = make_ind_file(ind_file, input)
198
199 par_file = os.path.join(output_files_path, 'par.admix')
200 evec_file = os.path.join(output_files_path, 'coordinates.txt')
201 eval_file = os.path.join(output_files_path, 'admix.eval')
202 make_par_file(par_file, geno_file, snp_file, ind_file, evec_file, eval_file)
203
204 smartpca_stats = do_smartpca(par_file)
205
206 do_ploteig(evec_file, population_names)
207 plot_file = 'coordinates.txt.1:2.{0}.pdf'.format(':'.join(population_names))
208 output_plot_file = os.path.join(output_files_path, 'PCA.pdf')
209 shutil.copy2(plot_file, output_plot_file)
210 os.unlink(plot_file)
211
212 do_eval2pct(eval_file, os.path.join(output_files_path, 'explained.txt'))
213 os.unlink(eval_file)
214
215 do_coords2admix(evec_file)
216
217 ################################################################################
218
219 info_page = gd_composite.InfoPage()
220 info_page.set_title('PCA Galaxy Composite Dataset')
221
222 display_file = gd_composite.DisplayFile()
223 display_value = gd_composite.DisplayValue()
224
225 out_pdf = gd_composite.Parameter(name='PCA.pdf', value='PCA.pdf', display_type=display_file)
226 out_evec = gd_composite.Parameter(name='coordinates.txt', value='coordinates.txt', display_type=display_file)
227 out_explained = gd_composite.Parameter(name='explained.txt', value='explained.txt', display_type=display_file)
228
229 evec_prefix = 'coordinates.txt.1:2.{0}'.format(':'.join(population_names))
230 ps_file = '{0}.ps'.format(evec_prefix)
231 xtxt_file = '{0}.xtxt'.format(evec_prefix)
232
233 os.unlink(os.path.join(output_files_path, ps_file))
234 os.unlink(os.path.join(output_files_path, xtxt_file))
235
236 info_page.add_output_parameter(out_pdf)
237 info_page.add_output_parameter(out_evec)
238 info_page.add_output_parameter(out_explained)
239
240 in_admix = gd_composite.Parameter(name='par.admix', value='par.admix', display_type=display_file)
241 in_geno = gd_composite.Parameter(name='admix.geno', value='admix.geno', display_type=display_file)
242 in_snp = gd_composite.Parameter(name='admix.snp', value='admix.snp', display_type=display_file)
243 in_ind = gd_composite.Parameter(name='admix.ind', value='admix.ind', display_type=display_file)
244
245 info_page.add_input_parameter(in_admix)
246 info_page.add_input_parameter(in_geno)
247 info_page.add_input_parameter(in_snp)
248 info_page.add_input_parameter(in_ind)
249
250 misc_stats = gd_composite.Parameter(description='Stats<p/><pre>\n{0}\n</pre>'.format(smartpca_stats), display_type=display_value)
251
252 info_page.add_misc(misc_stats)
253
254 with open (output, 'w') as ofh:
255 print >> ofh, info_page.render()
256
257 sys.exit(0)
258