diff nucleotide_diversity_pi.py @ 22:95a05c1ef5d5

update to devshed revision aaece207bd01

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nucleotide_diversity_pi.py	Mon Mar 11 11:28:06 2013 -0400
@@ -0,0 +1,64 @@
+#!/usr/bin/env python
+
+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 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:]
+
+p_total = Population()
+p_total.from_tag_list(individual_metadata)
+
+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)
+
+################################################################################
+
+prog = 'get_pi'
+
+args = [ prog ]
+args.append(gd_saps_file)
+args.append(gd_snps_file)
+args.append(covered_intervals_file)
+
+columns = p1.column_list()
+for column in columns:
+    args.append('{0}'.format(column))
+
+run_program(None, args, stdout_file=output_file)
+
+sys.exit(0)
+