diff rename_individuals.py @ 0:99a67ac88802 default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rename_individuals.py	Thu Apr 05 14:22:50 2012 -0400
@@ -0,0 +1,33 @@
+#!/usr/bin/env python
+
+import sys
+from Population import Population
+
+input_file, output_file = sys.argv[1:3]
+tags = sys.argv[3:]
+
+aliases = {}
+
+for tag in tags:
+    column, alias = tag.split(':', 1)
+    column = column.strip()
+    alias = alias.strip()
+    if alias:
+        aliases[column] = alias
+
+p_total = Population()
+p_total.from_population_file(input_file)
+
+with open(output_file, 'w') as ofh:
+    for column in p_total.column_list():
+        individual = p_total.individual_with_column(column)
+        real_name = individual.real_name
+        rv = [column, real_name, '']
+        if column in aliases:
+            alias = aliases[column]
+            if alias != real_name:
+                rv[2] = alias
+        print >> ofh, '\t'.join(rv)
+
+sys.exit(0)
+