Mercurial > repos > miller-lab > genome_diversity

comparison prepare_population_structure.py @ 17:a3af29edcce2

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Uploaded Miller Lab Devshed version a51c894f5bed
author miller-lab
date Fri, 28 Sep 2012 11:57:18 -0400
parents 2c498d40ecde
children 248b06e86022
comparison
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16:be0e2223c531 17:a3af29edcce2
1 #!/usr/bin/env python
2
3 import errno
4 import os
5 import shutil
6 import subprocess
7 import sys
8 from Population import Population
9 import gd_composite
10
11 ################################################################################
12
13 def do_import(filename, files_path, min_reads, min_qual, min_spacing, tags, using_info, population_list):
14 info_page = gd_composite.InfoPage()
15 info_page.set_title('Prepare to look for population structure Galaxy Composite Dataset')
16
17 display_file = gd_composite.DisplayFile()
18 display_value = gd_composite.DisplayValue()
19
20 out_ped = gd_composite.Parameter(name='admix.ped', value='admix.ped', display_type=display_file)
21 out_map = gd_composite.Parameter(name='admix.map', value='admix.map', display_type=display_file)
22 out_use = gd_composite.Parameter(description=using_info, display_type=display_value)
23
24 info_page.add_output_parameter(out_ped)
25 info_page.add_output_parameter(out_map)
26 info_page.add_output_parameter(out_use)
27
28 in_min_reads = gd_composite.Parameter(description='Minimum reads covering a SNP, per individual', value=min_reads, display_type=display_value)
29 in_min_qual = gd_composite.Parameter(description='Minimum quality value, per individual', value=min_qual, display_type=display_value)
30 in_min_spacing = gd_composite.Parameter(description='Minimum spacing between SNPs on the same scaffold', value=min_spacing, display_type=display_value)
31
32 info_page.add_input_parameter(in_min_reads)
33 info_page.add_input_parameter(in_min_qual)
34 info_page.add_input_parameter(in_min_spacing)
35
36 misc_populations = gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList())
37 info_page.add_misc(misc_populations)
38
39 with open(filename, 'w') as ofh:
40 print >> ofh, info_page.render()
41
42 def mkdir_p(path):
43 try:
44 os.makedirs(path)
45 except OSError, e:
46 if e.errno <> errno.EEXIST:
47 raise
48
49 def die(message, exit=True):
50 print >> sys.stderr, message
51 if exit:
52 sys.exit(1)
53
54 ################################################################################
55
56 if len(sys.argv) < 9:
57 die("Usage")
58
59 # parse command line
60 input_snp_filename, min_reads, min_qual, min_spacing, output_filename, output_files_path = sys.argv[1:7]
61 args = sys.argv[7:]
62
63 individual_metadata = []
64 population_files = []
65 population_names = []
66 all_individuals = False
67
68 for arg in args:
69 if arg == 'all_individuals':
70 all_individuals = True
71 elif len(arg) > 11:
72 tag = arg[:11]
73 value = arg[11:]
74 if tag == 'individual:':
75 individual_metadata.append(value)
76 elif tag == 'population:':
77 filename, name = value.split(':', 1)
78 population_files.append(filename)
79 population_names.append(name)
80
81 p_total = Population()
82 p_total.from_tag_list(individual_metadata)
83
84 individual_population = {}
85
86 population_list = []
87
88 if all_individuals:
89 p1 = p_total
90 p1.name = 'All Individuals'
91 population_list.append(p1)
92 else:
93 p1 = Population()
94 for idx in range(len(population_files)):
95 population_file = population_files[idx]
96 population_name = population_names[idx]
97 this_pop = Population(population_name)
98 this_pop.from_population_file(population_file)
99 population_list.append(this_pop)
100 p1.from_population_file(population_file)
101 tags = p1.tag_list()
102 for tag in tags:
103 if tag not in individual_population:
104 individual_population[tag] = population_name
105
106 if not p_total.is_superset(p1):
107 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
108 sys.exit(1)
109
110 # run tool
111 prog = 'admix_prep'
112
113 args = []
114 args.append(prog)
115 args.append(input_snp_filename)
116 args.append(min_reads)
117 args.append(min_qual)
118 args.append(min_spacing)
119
120 tags = p1.tag_list()
121 for tag in tags:
122 args.append(tag)
123
124 #print "args:", ' '.join(args)
125 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=subprocess.PIPE, stderr=sys.stderr)
126 (stdoutdata, stderrdata) = p.communicate()
127 rc = p.returncode
128
129 if rc != 0:
130 die('admix_prep failed: rc={0}'.format(rc))
131
132 using_info = stdoutdata.rstrip('\r\n')
133 mkdir_p(output_files_path)
134 output_ped_filename = os.path.join(output_files_path, 'admix.ped')
135 output_map_filename = os.path.join(output_files_path, 'admix.map')
136 shutil.copy2('admix.ped', output_ped_filename)
137 shutil.copy2('admix.map', output_map_filename)
138 do_import(output_filename, output_files_path, min_reads, min_qual, min_spacing, tags, using_info, population_list)
139
140 os.unlink('admix.ped')
141 os.unlink('admix.map')
142
143 sys.exit(0)
144