--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/specify.py	Tue May 28 16:24:19 2013 -0400
@@ -0,0 +1,147 @@
+#!/usr/bin/env python
+
+import sys
+import base64
+
+def parse_args(args):
+    if len(args) < 3:
+        usage()
+
+    input_file, output_file = args[1:3]
+
+    individuals = []
+    checkboxes = []
+    strings = []
+
+    for arg in args[3:]:
+        if ':' in arg:
+            arg_type, arg = arg.split(':', 1)
+        else:
+            print >> sys.stderr, "unknown argument:", arg
+            usage()
+
+        if arg_type == 'individual':
+            individuals.append(arg)
+        elif arg_type == 'checkbox':
+            checkboxes.append(arg)
+        elif arg_type == 'string':
+            strings.append(arg)
+        else:
+            print >> sys.stderr, "unknown argument:", arg
+            usage()
+
+    return input_file, output_file, individuals, checkboxes, strings
+
+def usage():
+    print >> sys.stderr, "Usage: %s <input> <output> [<individual:col:name> ...] [<checkbox:col:name> ...] [<string:base64> ...]" % (sys.argv[0])
+    sys.exit(1)
+
+def parse_individuals(individuals):
+    ind_col2name = {}
+    ind_name2col = {}
+
+    for individual in individuals:
+        if ':' in individual:
+            column, name = individual.split(':', 1)
+        else:
+            print >> sys.stderr, "invalid individual specification:", individual
+            usage()
+
+        try:
+            column = int(column)
+        except:
+            print "individual column is not an integer:", individual
+            usage()
+
+        if column not in ind_col2name:
+            ind_col2name[column] = name
+        else:
+            if ind_col2name[column] != name:
+                print "duplicate individual column:", name, column, ind_col2name[column]
+                usage()
+
+        if name not in ind_name2col:
+            ind_name2col[name] = [column]
+        elif column not in ind_name2col[name]:
+            ind_name2col[name].append(column)
+
+    return ind_col2name, ind_name2col
+
+def parse_checkboxes(checkboxes, ind_col2name):
+    columns = []
+
+    for checkbox in checkboxes:
+        if ':' in checkbox:
+            column, name = checkbox.split(':', 1)
+        else:
+            print >> sys.stderr, "invalid checkbox specification:", checkbox
+            usage()
+
+        try:
+            column = int(column)
+        except:
+            print "checkbox column is not an integer:", checkbox
+            usage()
+
+        if column not in ind_col2name:
+            print "individual not in SNP table:", name
+            usage()
+
+        if column not in columns:
+            columns.append(column)
+
+    return columns
+
+def parse_strings(strings, ind_col2name, ind_name2col):
+    columns = []
+
+    for string in strings:
+        try:
+            decoded = base64.b64decode(string)
+        except:
+            print >> sys.stderr, "invalid base64 string:", string
+            usage()
+
+        names = find_names(decoded, ind_name2col.keys())
+        for name in names:
+            cols = ind_name2col[name]
+            if len(cols) == 1:
+                col = cols[0]
+                if col not in columns:
+                    columns.append(col)
+            else:
+                print >> sys.stderr, "name with multiple columns:", name
+                usage()
+
+    return columns
+
+def find_names(string, names):
+    rv = []
+    for name in names:
+        if name in string:
+            if name not in rv:
+                rv.append(name)
+    return rv
+
+
+
+
+input_file, output_file, individuals, checkboxes, strings = parse_args(sys.argv)
+ind_col2name, ind_name2col = parse_individuals(individuals)
+cb_cols = parse_checkboxes(checkboxes, ind_col2name)
+str_cols = parse_strings(strings, ind_col2name, ind_name2col)
+
+out_cols = cb_cols
+for col in str_cols:
+    if col not in out_cols:
+        out_cols.append(col)
+
+with open(output_file, 'w') as fh:
+    for col in sorted(out_cols):
+        print >> fh, '\t'.join([str(x) for x in [col, ind_col2name[col], '']])
+
+sys.exit(0)
+
+
+
+