diff nucleotide_diversity_pi.py @ 27:8997f2ca8c7a

Update to Miller Lab devshed revision bae0d3306d3b

--- a/nucleotide_diversity_pi.py	Mon Jun 03 12:29:29 2013 -0400
+++ b/nucleotide_diversity_pi.py	Mon Jul 15 10:47:35 2013 -0400
@@ -1,49 +1,23 @@
 #!/usr/bin/env python
 
+import gd_util
 import sys
-import subprocess
 from Population import Population
 
 ################################################################################
 
-def run_program(prog, args, stdout_file=None, space_to_tab=False):
-    #print "args: ", ' '.join(args)
-    p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
-    (stdoutdata, stderrdata) = p.communicate()
-    rc = p.returncode
+if len(sys.argv) != 7:
+    gd_util.die('Usage')
 
-    if stdout_file is not None:
-        with open(stdout_file, 'w') as ofh:
-            lines = stdoutdata.split('\n')
-            for line in lines:
-                line = line.strip()
-                if line:
-                    if space_to_tab:
-                        line = line.replace(' ', '\t')
-                    print >> ofh, line
-
-    if rc != 0:
-        print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
-        print >> sys.stderr, stderrdata
-        sys.exit(1)
-
-################################################################################
-
-if len(sys.argv) < 8:
-    print >> sys.stderr, "Usage"
-    sys.exit(1)
-
-gd_saps_file, gd_snps_file, covered_intervals_file, gd_indivs_file, output_file = sys.argv[1:6]
-individual_metadata = sys.argv[6:]
+gd_saps_file, gd_snps_file, covered_intervals_file, gd_indivs_file, output_file, 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(gd_indivs_file)
 if not p_total.is_superset(p1):
-    print >> sys.stderr, 'There is an individual in the population individuals that is not in the SNP table'
-    sys.exit(1)
+    gd_util.die('There is an individual in the population individuals that is not in the SNP table')
 
 ################################################################################
 
@@ -56,9 +30,10 @@
 
 columns = p1.column_list()
 for column in columns:
-    args.append('{0}'.format(column))
+    args.append(column)
 
-run_program(None, args, stdout_file=output_file)
+with open(output_file, 'w') as fh:
+    gd_util.run_program(prog, args, stdout=fh)
 
 sys.exit(0)