--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenetic_tree.py	Mon Apr 09 12:03:06 2012 -0400
@@ -0,0 +1,219 @@
+#!/usr/bin/env python
+
+import os
+import errno
+import sys
+import subprocess
+import shutil
+from Population import Population
+import gd_composite
+
+################################################################################
+
+def mkdir_p(path):
+  try:
+    os.makedirs(path)
+  except OSError, e:
+    if e.errno <> errno.EEXIST:
+      raise
+
+################################################################################
+
+if len(sys.argv) < 11:
+    print >> sys.stderr, "Usage"
+    sys.exit(1)
+
+input, p1_input, output, extra_files_path, minimum_coverage, minimum_quality, dbkey, data_source, draw_tree_options = sys.argv[1:10]
+
+individual_metadata = sys.argv[10:]
+
+# note: TEST THIS
+if dbkey in ['', '?', 'None']:
+    dbkey = 'none'
+
+p_total = Population()
+p_total.from_tag_list(individual_metadata)
+
+
+################################################################################
+
+mkdir_p(extra_files_path)
+
+################################################################################
+
+def run_program(prog, args, ofh):
+    #print "args: ", ' '.join(args)
+    p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=ofh, stderr=subprocess.PIPE)
+    (stdoutdata, stderrdata) = p.communicate()
+    rc = p.returncode
+    ofh.close()
+
+    if rc != 0:
+        #print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
+        print >> sys.stderr, stderrdata
+        sys.exit(1)
+
+################################################################################
+
+phylip_outfile = os.path.join(extra_files_path, 'distance_matrix.phylip')
+newick_outfile = os.path.join(extra_files_path, 'phylogenetic_tree.newick')
+ps_outfile = 'tree.ps'
+pdf_outfile = os.path.join(extra_files_path, 'tree.pdf')
+
+################################################################################
+
+informative_snp_file = os.path.join(extra_files_path, 'informative_snps.txt')
+mega_distance_matrix_file = os.path.join(extra_files_path, 'mega_distance_matrix.txt')
+
+prog = 'dist_mat'
+
+args = []
+args.append(prog)
+args.append(input)
+args.append(minimum_coverage)
+args.append(minimum_quality)
+args.append(dbkey)
+args.append(data_source)
+args.append(informative_snp_file)
+args.append(mega_distance_matrix_file)
+
+if p1_input == "all_individuals":
+    tags = p_total.tag_list()
+else:
+    p1 = Population()
+    p1.from_population_file(p1_input)
+    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)
+    tags = p1.tag_list()
+
+for tag in tags:
+    args.append(tag)
+
+fh = open(phylip_outfile, 'w')
+run_program(None, args, fh)
+
+################################################################################
+
+prog = 'quicktree'
+
+args = []
+args.append(prog)
+args.append('-in')
+args.append('m')
+args.append('-out')
+args.append('t')
+args.append(phylip_outfile)
+
+fh = open(newick_outfile, 'w')
+run_program(None, args, fh)
+
+################################################################################
+
+prog = 'draw_tree'
+
+args = []
+args.append(prog)
+if draw_tree_options:
+    args.append(draw_tree_options)
+args.append(newick_outfile)
+
+fh = open(ps_outfile, 'w')
+run_program(None, args, fh)
+
+################################################################################
+
+prog = 'ps2pdf'
+
+args = []
+args.append(prog)
+args.append('-dPDFSETTINGS=/prepress')
+args.append(ps_outfile)
+args.append('-')
+
+fh = open(pdf_outfile, 'w')
+run_program(None, args, fh)
+
+shutil.copyfile(pdf_outfile, output)
+
+################################################################################
+
+info_page = gd_composite.InfoPage()
+info_page.set_title('Phylogenetic tree Galaxy Composite Dataset')
+
+display_file = gd_composite.DisplayFile()
+display_value = gd_composite.DisplayValue()
+
+out_pdf = gd_composite.Parameter(name='tree.pdf', value='tree.pdf', display_type=display_file)
+out_newick = gd_composite.Parameter(value='phylogenetic_tree.newick', name='phylogenetic tree (newick)', display_type=display_file)
+out_phylip = gd_composite.Parameter(value='distance_matrix.phylip', name='Phylip distance matrix', display_type=display_file)
+out_mega = gd_composite.Parameter(value='mega_distance_matrix.txt', name='Mega distance matrix', display_type=display_file)
+out_snps = gd_composite.Parameter(value='informative_snps.txt', name='informative SNPs', display_type=display_file)
+
+info_page.add_output_parameter(out_pdf)
+info_page.add_output_parameter(out_newick)
+info_page.add_output_parameter(out_phylip)
+info_page.add_output_parameter(out_mega)
+info_page.add_output_parameter(out_snps)
+
+in_min_cov = gd_composite.Parameter(description='Minimum coverage', value=minimum_coverage, display_type=display_value)
+in_min_qual = gd_composite.Parameter(description='Minimum quality', value=minimum_quality, display_type=display_value)
+
+include_ref_value = 'no'
+if dbkey != 'none':
+    include_ref_value = 'yes'
+
+in_include_ref = gd_composite.Parameter(description='Include reference sequence', value=include_ref_value, display_type=display_value)
+
+if data_source == '0':
+    data_source_value = 'sequence coverage'
+elif data_source == '1':
+    data_source_value = 'estimated genotype'
+
+in_data_source = gd_composite.Parameter(description='Data source', value=data_source_value, display_type=display_value)
+
+branch_type_value = 'square'
+if 'd' in draw_tree_options:
+    branch_type_value = 'diagonal'
+
+in_branch_type = gd_composite.Parameter(description='Branch type', value=branch_type_value, display_type=display_value)
+
+branch_scale_value = 'yes'
+if 's' in draw_tree_options:
+    branch_scale_value = 'no'
+
+in_branch_scale = gd_composite.Parameter(description='Draw branches to scale', value=branch_scale_value, display_type=display_value)
+
+branch_length_value = 'yes'
+if 'b' in draw_tree_options:
+    branch_length_value = 'no'
+
+in_branch_length = gd_composite.Parameter(description='Show branch lengths', value=branch_length_value, display_type=display_value)
+
+tree_layout_value = 'horizontal'
+if 'v' in draw_tree_options:
+    tree_layout_value = 'vertical'
+
+in_tree_layout = gd_composite.Parameter(description='Tree layout', value=tree_layout_value, display_type=display_value)
+
+info_page.add_input_parameter(in_min_cov)
+info_page.add_input_parameter(in_min_qual)
+info_page.add_input_parameter(in_include_ref)
+info_page.add_input_parameter(in_data_source)
+info_page.add_input_parameter(in_branch_type)
+info_page.add_input_parameter(in_branch_scale)
+info_page.add_input_parameter(in_branch_length)
+info_page.add_input_parameter(in_tree_layout)
+
+misc_individuals = gd_composite.Parameter(name='Individuals', value=tags, display_type=gd_composite.DisplayTagList())
+
+info_page.add_misc(misc_individuals)
+
+
+with open(output, 'w') as ofh:
+    print >> ofh, info_page.render()
+
+################################################################################
+
+sys.exit(0)
+