--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/new_operations/subtract_query.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,106 @@
+#!/usr/bin/env python
+# Greg Von Kuster
+
+"""
+Subtract an entire query from another query
+usage: %prog in_file_1 in_file_2 begin_col end_col output 
+"""
+import sys, re
+from galaxy import eggs
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+
+# Older py compatibility
+try:
+    set()
+except:
+    from sets import Set as set
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def get_lines(fname, begin_col='', end_col=''):
+    lines = set([])
+    i = 0
+    for i, line in enumerate(file(fname)):
+        line = line.rstrip('\r\n')
+        if line and not line.startswith('#'):
+            if begin_col and end_col:
+                """Both begin_col and end_col must be integers at this point."""
+                try:
+                    line = line.split('\t')
+                    line = '\t'.join([line[j] for j in range(begin_col-1, end_col)])
+                    lines.add( line )
+                except: pass
+            else:
+                lines.add( line )
+    if i: return (i+1, lines)
+    else: return (i, lines)
+
+def main():
+    
+    # Parsing Command Line here
+    options, args = doc_optparse.parse( __doc__ )
+
+    try:
+        inp1_file, inp2_file, begin_col, end_col, out_file = args
+    except:
+        doc_optparse.exception()
+    
+    begin_col = begin_col.strip()
+    end_col = end_col.strip()
+    
+    if begin_col != 'None' or end_col != 'None':
+        """
+        The user selected columns for restriction.  We'll allow default
+        values for both begin_col and end_col as long as the user selected
+        at least one of them for restriction.
+        """
+        if begin_col == 'None':
+            begin_col = end_col
+        elif end_col == 'None':
+            end_col = begin_col
+        begin_col = int(begin_col)
+        end_col = int(end_col)
+        """Make sure that begin_col <= end_col (switch if not)"""
+        if begin_col > end_col:
+            tmp_col = end_col
+            end_col = begin_col
+            begin_col = tmp_col
+    else:
+        begin_col = end_col = ''
+
+    try:
+        fo = open(out_file,'w')
+    except:
+        print >> sys.stderr, "Unable to open output file"
+        sys.exit()
+
+    """
+    len1 is the number of lines in inp1_file
+    lines1 is the set of unique lines in inp1_file
+    diff1 is the number of duplicate lines removed from inp1_file
+    """
+    len1, lines1 = get_lines(inp1_file, begin_col, end_col)
+    diff1 = len1 - len(lines1)
+    len2, lines2 = get_lines(inp2_file, begin_col, end_col)
+    
+    lines1.difference_update(lines2)
+    """lines1 is now the set of unique lines in inp1_file - the set of unique lines in inp2_file"""
+
+    for line in lines1:
+        print >> fo, line
+
+    fo.close()
+    
+    info_msg = 'Subtracted %d lines. ' %((len1 - diff1) - len(lines1))
+    
+    if begin_col and end_col:
+        info_msg += 'Restricted to columns c' + str(begin_col) + ' thru c' + str(end_col) + '. '
+
+    if diff1 > 0:
+        info_msg += 'Eliminated %d duplicate/blank/comment/invalid lines from first query.' %diff1
+    
+    print info_msg
+
+if __name__ == "__main__":
+    main()