--- a/phylogenetic_tree.py	Mon Jun 03 12:29:29 2013 -0400
+++ b/phylogenetic_tree.py	Mon Jul 15 10:47:35 2013 -0400
@@ -1,154 +1,63 @@
 #!/usr/bin/env python
 
+import gd_util
 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) != 12:
+    gd_util.die('Usage')
 
-#  <command interpreter="python">
-#    phylogenetic_tree.py "$input" "$output" "$output.files_path"
-#
-#    #if $input_type.choice == '0'
-#      "gd_snp"
-#      #if $input_type.data_source.choice == '0'
-#        "sequence_coverage"
-#        "$input_type.data_source.minimum_coverage"
-#        "$input_type.data_source.minimum_quality"
-#      #else if $input_type.data_source.choice == '1'
-#        "estimated_genotype"
-#    #else if $input_type.choice == '1'
-#      "gd_genotype"
-#    #end if
-#
-#    #if $individuals.choice == '0'
-#      "all_individuals"
-#    #else if $individuals.choice == '1'
-#      "$individuals.p1_input"
-#    #end if
-#
-#    #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
-#        "none"
-#    #else
-#        "$input.metadata.dbkey"
-#    #end if
-#
-#    #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
-#    #if $draw_tree_options == ''
-#        ""
-#    #else
-#        "-$draw_tree_options"
-#    #end if
-#
-#    #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
-#        #set $arg = '%s:%s' % ($individual_col, $individual_name)
-#        "$arg"
-#    #end for
-#  </command>
-
-################################################################################
-
-# 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)
-
-if len(sys.argv) < 5:
-    print >> sys.stderr, 'Usage'
-    sys.exit(1)
-
-input, output, extra_files_path, input_type = sys.argv[1:5]
-args = sys.argv[5:]
-
-data_source = '1'
-minimum_coverage = '0'
-minimum_quality = '0'
+input, output, extra_files_path, input_type, data_source_arg, minimum_coverage, minimum_quality, p1_input, dbkey, draw_tree_options, ind_arg = sys.argv[1:]
 
 if input_type == 'gd_snp':
-    data_source_arg = args.pop(0)
     if data_source_arg == 'sequence_coverage':
-        data_source = '0'
-        minimum_coverage = args.pop(0)
-        minimum_quality = args.pop(0)
+        data_source = 0
     elif data_source_arg == 'estimated_genotype':
-        pass
+        data_source = 1
     else:
-        print >> sys.stderr, 'Unsupported data_source:', data_source_arg
-        sys.exit(1)
+        gd_util.die('Unsupported data_source: {0}'.format(data_source_arg))
 elif input_type == 'gd_genotype':
-    pass
+        data_source = 1
+        minimum_coverage = 0
+        minimum_quality = 0
 else:
-    print >> sys.stderr, 'Unsupported input_type:', input_type
-    sys.exit(1)
-
-p1_input, dbkey, draw_tree_options = args[:3]
+    gd_util.die('Unsupported input_type:: {0}'.format(input_type))
 
 # note: TEST THIS
 if dbkey in ['', '?', 'None']:
     dbkey = 'none'
 
-individual_metadata = args[3:]
+p_total = Population()
+p_total.from_wrapped_dict(ind_arg)
 
-p_total = Population()
-p_total.from_tag_list(individual_metadata)
-
-################################################################################
-
-mkdir_p(extra_files_path)
+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):
+        gd_util.die('There is an individual in the population that is not in the SNP table')
+    tags = p1.tag_list()
 
 ################################################################################
 
-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)
-
-################################################################################
-
+gd_util.mkdir_p(extra_files_path)
 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')
 
 ################################################################################
 
-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 = [ prog ]
 args.append(input)
 args.append(minimum_coverage)
 args.append(minimum_quality)
@@ -157,67 +66,53 @@
 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:
     if input_type == 'gd_genotype':
         column, name = tag.split(':')
         tag = '{0}:{1}'.format(int(column) - 2, name)
     args.append(tag)
 
-fh = open(phylip_outfile, 'w')
-run_program(None, args, fh)
+with open(phylip_outfile, 'w') as fh:
+    gd_util.run_program(prog, args, stdout=fh)
 
 ################################################################################
 
 prog = 'quicktree'
 
-args = []
-args.append(prog)
+args = [ 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)
+with open(newick_outfile, 'w') as fh:
+    gd_util.run_program(prog, args, stdout=fh)
 
 ################################################################################
 
 prog = 'draw_tree'
 
-args = []
-args.append(prog)
+args = [ prog ]
+
 if draw_tree_options:
     args.append(draw_tree_options)
+
 args.append(newick_outfile)
 
-fh = open(ps_outfile, 'w')
-run_program(None, args, fh)
+with open(ps_outfile, 'w') as fh:
+    gd_util.run_program(prog, args, stdout=fh)
 
 ################################################################################
 
 prog = 'ps2pdf'
 
-args = []
-args.append(prog)
+args = [ prog ]
 args.append('-dPDFSETTINGS=/prepress')
 args.append(ps_outfile)
-args.append('-')
+args.append(pdf_outfile)
 
-fh = open(pdf_outfile, 'w')
-run_program(None, args, fh)
-
-shutil.copyfile(pdf_outfile, output)
+gd_util.run_program(prog, args)
 
 ################################################################################
 
@@ -248,9 +143,9 @@
 
 in_include_ref = gd_composite.Parameter(description='Include reference sequence', value=include_ref_value, display_type=display_value)
 
-if data_source == '0':
+if data_source == 0:
     data_source_value = 'sequence coverage'
-elif data_source == '1':
+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)