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comparison dpmix.py @ 9:22fe0154fa54

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added support for heterochromatic regions
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 10 Jul 2012 11:41:22 -0400
parents 2c498d40ecde
children
comparison
equal deleted inserted replaced
8:30771a097f14 9:22fe0154fa54
5 import os 5 import os
6 import subprocess 6 import subprocess
7 from Population import Population 7 from Population import Population
8 import gd_composite 8 import gd_composite
9 from dpmix_plot import make_dpmix_plot 9 from dpmix_plot import make_dpmix_plot
10 from LocationFile import LocationFile
10 11
11 ################################################################################ 12 ################################################################################
12 13
13 def mkdir_p(path): 14 def mkdir_p(path):
14 try: 15 try:
38 print >> sys.stderr, stderrdata 39 print >> sys.stderr, stderrdata
39 sys.exit(1) 40 sys.exit(1)
40 41
41 ################################################################################ 42 ################################################################################
42 43
43 if len(sys.argv) < 14: 44 if len(sys.argv) < 15:
44 print "usage" 45 print "usage"
45 sys.exit(1) 46 sys.exit(1)
46 47
47 input, data_source, switch_penalty, ap1_input, ap2_input, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir = sys.argv[1:13] 48 input, data_source, switch_penalty, ap1_input, ap2_input, p_input, output, output2, output2_dir, dbkey, ref_column, galaxy_data_index_dir, heterochromatin_loc_file = sys.argv[1:14]
48 individual_metadata = sys.argv[13:] 49 individual_metadata = sys.argv[14:]
49 50
50 chrom = 'all' 51 chrom = 'all'
51 analyze_additional = '0'
52 add_logs = '0' 52 add_logs = '0'
53
54 loc_path = os.path.join(galaxy_data_index_dir, heterochromatin_loc_file)
55 location_file = LocationFile(loc_path)
56 heterochrom_path = location_file.get_values_if_exists(dbkey)
57 if heterochrom_path is None:
58 heterochrom_path = '/dev/null'
53 59
54 population_list = [] 60 population_list = []
55 61
56 p_total = Population() 62 p_total = Population()
57 p_total.from_tag_list(individual_metadata) 63 p_total.from_tag_list(individual_metadata)
91 args.append(ref_column) 97 args.append(ref_column)
92 args.append(chrom) 98 args.append(chrom)
93 args.append(data_source) 99 args.append(data_source)
94 args.append(add_logs) 100 args.append(add_logs)
95 args.append(switch_penalty) 101 args.append(switch_penalty)
96 args.append(analyze_additional) 102 args.append(heterochrom_path)
97 args.append(misc_file) 103 args.append(misc_file)
98 104
99 columns = ap1.column_list() 105 columns = ap1.column_list()
100 for column in columns: 106 for column in columns:
101 args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name)) 107 args.append('{0}:1:{1}'.format(column, ap1.individual_with_column(column).name))
136 if data_source == '0': 142 if data_source == '0':
137 data_source_value = 'sequence coverage' 143 data_source_value = 'sequence coverage'
138 elif data_source == '1': 144 elif data_source == '1':
139 data_source_value = 'estimated genotype' 145 data_source_value = 'estimated genotype'
140 146
141 if analyze_additional == '0':
142 analyze_additional_value = 'no'
143 elif analyze_additional == '1':
144 analyze_additional_value = 'yes'
145
146 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value) 147 in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)
147 in_switch_penalty = gd_composite.Parameter(description='Switch penalty', value=switch_penalty, display_type=display_value) 148 in_switch_penalty = gd_composite.Parameter(description='Switch penalty', value=switch_penalty, display_type=display_value)
148 in_analyze_additional = gd_composite.Parameter(description='Also analyze random chromosome', value=analyze_additional_value, display_type=display_value)
149 149
150 info_page.add_input_parameter(in_data_source) 150 info_page.add_input_parameter(in_data_source)
151 info_page.add_input_parameter(in_switch_penalty) 151 info_page.add_input_parameter(in_switch_penalty)
152 info_page.add_input_parameter(in_analyze_additional)
153 152
154 misc_populations = gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList()) 153 misc_populations = gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList())
155 154
156 info_page.add_misc(misc_populations) 155 info_page.add_misc(misc_populations)
157 156