--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prepare_population_structure.py	Fri Sep 28 11:57:18 2012 -0400
@@ -0,0 +1,144 @@
+#!/usr/bin/env python
+
+import errno
+import os
+import shutil
+import subprocess
+import sys
+from Population import Population
+import gd_composite
+
+################################################################################
+
+def do_import(filename, files_path, min_reads, min_qual, min_spacing, tags, using_info, population_list):
+    info_page = gd_composite.InfoPage()
+    info_page.set_title('Prepare to look for population structure Galaxy Composite Dataset')
+
+    display_file = gd_composite.DisplayFile()
+    display_value = gd_composite.DisplayValue()
+
+    out_ped = gd_composite.Parameter(name='admix.ped', value='admix.ped', display_type=display_file)
+    out_map = gd_composite.Parameter(name='admix.map', value='admix.map', display_type=display_file)
+    out_use = gd_composite.Parameter(description=using_info, display_type=display_value)
+
+    info_page.add_output_parameter(out_ped)
+    info_page.add_output_parameter(out_map)
+    info_page.add_output_parameter(out_use)
+
+    in_min_reads = gd_composite.Parameter(description='Minimum reads covering a SNP, per individual', value=min_reads, display_type=display_value)
+    in_min_qual = gd_composite.Parameter(description='Minimum quality value, per individual', value=min_qual, display_type=display_value)
+    in_min_spacing = gd_composite.Parameter(description='Minimum spacing between SNPs on the same scaffold', value=min_spacing, display_type=display_value)
+
+    info_page.add_input_parameter(in_min_reads)
+    info_page.add_input_parameter(in_min_qual)
+    info_page.add_input_parameter(in_min_spacing)
+
+    misc_populations = gd_composite.Parameter(name='Populations', value=population_list, display_type=gd_composite.DisplayPopulationList())
+    info_page.add_misc(misc_populations)
+
+    with open(filename, 'w') as ofh:
+        print >> ofh, info_page.render()
+
+def mkdir_p(path):
+    try:
+        os.makedirs(path)
+    except OSError, e:
+        if e.errno <> errno.EEXIST:
+            raise
+
+def die(message, exit=True):
+    print >> sys.stderr, message
+    if exit:
+        sys.exit(1)
+
+################################################################################
+
+if len(sys.argv) < 9:
+    die("Usage")
+
+# parse command line
+input_snp_filename, min_reads, min_qual, min_spacing, output_filename, output_files_path = sys.argv[1:7]
+args = sys.argv[7:]
+
+individual_metadata = []
+population_files = []
+population_names = []
+all_individuals = False
+
+for arg in args:
+    if arg == 'all_individuals':
+        all_individuals = True
+    elif len(arg) > 11:
+        tag = arg[:11]
+        value = arg[11:]
+        if tag == 'individual:':
+            individual_metadata.append(value)
+        elif tag == 'population:':
+            filename, name = value.split(':', 1)
+            population_files.append(filename)
+            population_names.append(name)
+
+p_total = Population()
+p_total.from_tag_list(individual_metadata)
+
+individual_population = {}
+
+population_list = []
+
+if all_individuals:
+    p1 = p_total
+    p1.name = 'All Individuals'
+    population_list.append(p1)
+else:
+    p1 = Population()
+    for idx in range(len(population_files)):
+        population_file = population_files[idx]
+        population_name = population_names[idx]
+        this_pop = Population(population_name)
+        this_pop.from_population_file(population_file)
+        population_list.append(this_pop)
+        p1.from_population_file(population_file)
+        tags = p1.tag_list()
+        for tag in tags:
+            if tag not in individual_population:
+                individual_population[tag] = population_name
+
+if not p_total.is_superset(p1):
+    print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
+    sys.exit(1)
+
+# run tool
+prog = 'admix_prep'
+
+args = []
+args.append(prog)
+args.append(input_snp_filename)
+args.append(min_reads)
+args.append(min_qual)
+args.append(min_spacing)
+
+tags = p1.tag_list()
+for tag in tags:
+    args.append(tag)
+
+#print "args:", ' '.join(args)
+p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=subprocess.PIPE, stderr=sys.stderr)
+(stdoutdata, stderrdata) = p.communicate()
+rc = p.returncode
+
+if rc != 0:
+    die('admix_prep failed: rc={0}'.format(rc))
+
+using_info = stdoutdata.rstrip('\r\n')
+mkdir_p(output_files_path)
+output_ped_filename = os.path.join(output_files_path, 'admix.ped')
+output_map_filename = os.path.join(output_files_path, 'admix.map')
+shutil.copy2('admix.ped', output_ped_filename)
+shutil.copy2('admix.map', output_map_filename)
+do_import(output_filename, output_files_path, min_reads, min_qual, min_spacing, tags, using_info, population_list)
+
+os.unlink('admix.ped')
+os.unlink('admix.map')
+
+sys.exit(0)
+