diff reorder.py @ 24:248b06e86022

Added gd_genotype datatype. Modified tools to support new datatype.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/reorder.py	Tue May 28 16:24:19 2013 -0400
@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+
+import sys
+
+def parse_rangelist(string):
+    rv = []
+
+    tokens = strip_split(string, ',')
+    for token in tokens:
+        int_list = parse_token(token)
+        for int_val in int_list:
+            int_val -= 1
+            if int_val not in rv:
+                rv.append(int_val)
+
+    return rv
+
+def parse_token(token):
+    values = strip_split(token, '-')
+    num_values = len(values)
+
+    if num_values not in [1, 2]:
+        print >> sys.stderr, 'Error: "%s" is not a valid range' % token
+        sys.exit(1)
+
+    int_list = []
+    for value in values:
+        if value:
+            int_val = as_int(value)
+
+            if int_val < 1:
+                print >> sys.stderr, 'Error: "%s" is not >= 1' % value
+                sys.exit(1)
+
+            int_list.append(int_val)
+        else:
+            print >> sys.stderr, 'Error: "%s" is not a valid range' % token
+            sys.exit(1)
+
+    if num_values == 1:
+        return int_list
+
+    a, b = int_list
+
+    if a <= b:
+        return range(a, b+1)
+    else:
+        return range(a, b-1, -1)
+
+def strip_split(string, delim):
+    return [elem.strip() for elem in string.split(delim)]
+
+def as_int(string):
+    try:
+        val = int(string)
+    except:
+        print >> sys.stderr, 'Error: "%s" does not appear to be an integer' % string
+        sys.exit(1)
+    return val
+
+def get_lines(filename):
+    rv = []
+
+    fh = open(filename)
+    for line in fh:
+        line = line.rstrip('\r\n')
+        rv.append(line)
+    fh.close()
+
+    return rv
+
+def reorder(old_lines, new_order, filename):
+    max_index = len(old_lines) - 1
+
+    fh = open(filename, 'w')
+
+    for index in new_order:
+        if index <= max_index:
+            print >> fh, old_lines[index]
+            old_lines[index] = None
+
+    for line in old_lines:
+        if line is not None:
+            print >> fh, line
+
+    fh.close()
+
+if len(sys.argv) != 4:
+    print >> sys.stderr, "Usage"
+    sys.exit(1)
+
+input, output, order_string = sys.argv[1:]
+
+new_order = parse_rangelist(order_string)
+old_lines = get_lines(input)
+reorder(old_lines, new_order, output)
+
+sys.exit(0)