diff add_fst_column.py @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

--- a/add_fst_column.py	Mon Jun 03 12:29:29 2013 -0400
+++ b/add_fst_column.py	Mon Jul 15 10:47:35 2013 -0400
@@ -1,49 +1,36 @@
 #!/usr/bin/env python
 
-#  <command interpreter="python">
-#    add_fst_column.py "$input" "$p1_input" "$p2_input" "$data_source.choice" "$data_source.min_value" "$retain" "$discard_fixed" "$biased" "$output"
-#    #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
-#        #set $arg = '%s:%s' % ($individual_col, $individual)
-#        "$arg"
-#    #end for
-#  </command>
-
+import gd_util
 import sys
-import subprocess
 from Population import Population
 
 ################################################################################
 
-if len(sys.argv) < 12:
-    print >> sys.stderr, "Usage"
-    sys.exit(1)
+if len(sys.argv) != 13:
+    gd_util.die('Usage')
 
-input, p1_input, p2_input, input_type, genotypes, min_reads, min_qual, retain, discard_fixed, biased, output = sys.argv[1:12]
-individual_metadata = sys.argv[12:]
+input, p1_input, p2_input, input_type, data_source, min_reads, min_qual, retain, discard_fixed, biased, output, ind_arg = sys.argv[1:]
 
 p_total = Population()
-p_total.from_tag_list(individual_metadata)
+p_total.from_wrapped_dict(ind_arg)
 
 p1 = Population()
 p1.from_population_file(p1_input)
 if not p_total.is_superset(p1):
-    print >> sys.stderr, 'There is an individual in population 1 that is not in the SNP table'
-    sys.exit(1)
+    gd_util.die('There is an individual in population 1 that is not in the SNP table')
 
 p2 = Population()
 p2.from_population_file(p2_input)
 if not p_total.is_superset(p2):
-    print >> sys.stderr, 'There is an individual in population 2 that is not in the SNP table'
-    sys.exit(1)
+    gd_util.die('There is an individual in population 2 that is not in the SNP table')
 
 ################################################################################
 
 prog = 'Fst_column'
 
-args = []
-args.append(prog)
+args = [ prog ]
 args.append(input)
-args.append(genotypes)
+args.append(data_source)
 args.append(min_reads)
 args.append(min_qual)
 args.append(retain)
@@ -62,12 +49,8 @@
         column = int(column) - 2
     args.append('{0}:2'.format(column))
 
-fh = open(output, 'w')
-
-#print "args:", ' '.join(args)
-p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
-rc = p.wait()
-fh.close()
+with open(output, 'w') as fh:
+    gd_util.run_program(prog, args, stdout=fh)
 
 sys.exit(0)