--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/stats/column_maker.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,118 @@
+#!/usr/bin/env python
+# This tool takes a tab-delimited textfile as input and creates another column in the file which is the result of
+# a computation performed on every row in the original file.  The tool will skip over invalid lines within the file,
+# informing the user about the number of lines skipped.  
+import sys, re, os.path
+from galaxy import eggs
+from galaxy.tools import validation
+from galaxy.datatypes import metadata
+from math import log,exp,sqrt,ceil,floor
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+inp_file = sys.argv[1]
+out_file = sys.argv[2]
+expr = sys.argv[3]
+round_result = sys.argv[4]
+try:
+    in_columns = int( sys.argv[5] )
+except:
+    stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
+if in_columns < 2:
+    # To be considered tabular, data must fulfill requirements of the sniff.is_column_based() method.
+    stop_err( "Missing or invalid 'columns' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
+try:
+    in_column_types = sys.argv[6].split( ',' )
+except:
+    stop_err( "Missing or invalid 'column_types' metadata value, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
+if len( in_column_types ) != in_columns:
+    stop_err( "The 'columns' metadata setting does not conform to the 'column_types' metadata setting, click the pencil icon in the history item and select the Auto-detect option to correct it.  This tool can only be used with tab-delimited data." )
+    
+# Unescape if input has been escaped
+mapped_str = {
+    '__lt__': '<',
+    '__le__': '<=',
+    '__eq__': '==',
+    '__ne__': '!=',
+    '__gt__': '>',
+    '__ge__': '>=',
+    '__sq__': '\'',
+    '__dq__': '"',
+}
+for key, value in mapped_str.items():
+    expr = expr.replace( key, value )
+
+# Prepare the column variable names and wrappers for column data types
+cols, type_casts = [], []
+for col in range( 1, in_columns + 1 ):
+    col_name = "c%d" % col
+    cols.append( col_name )
+    col_type = in_column_types[ col - 1 ].strip()
+    if round_result == 'no' and col_type == 'int':
+        col_type = 'float'
+    type_cast = "%s(%s)" % ( col_type, col_name )
+    type_casts.append( type_cast )
+        
+col_str = ', '.join( cols )    # 'c1, c2, c3, c4'
+type_cast_str = ', '.join( type_casts )  # 'str(c1), int(c2), int(c3), str(c4)'
+assign = "%s = line.split( '\\t' )" % col_str
+wrap = "%s = %s" % ( col_str, type_cast_str )
+skipped_lines = 0
+first_invalid_line = 0
+invalid_line = None
+lines_kept = 0
+total_lines = 0
+out = open( out_file, 'wt' )
+
+# Read input file, skipping invalid lines, and perform computation that will result in a new column
+code = '''
+for i, line in enumerate( file( inp_file ) ):
+    total_lines += 1
+    line = line.rstrip( '\\r\\n' )
+    if not line or line.startswith( '#' ):
+        skipped_lines += 1
+        if not invalid_line:
+            first_invalid_line = i + 1
+            invalid_line = line
+        continue
+    try:
+        %s
+        %s
+        new_val = %s
+        if round_result == "yes":
+            new_val = int( round( new_val ) )
+        new_line = line + '\\t' + str( new_val )
+        print >> out, new_line
+        lines_kept += 1
+    except:
+        skipped_lines += 1
+        if not invalid_line:
+            first_invalid_line = i + 1
+            invalid_line = line
+''' % ( assign, wrap, expr )
+
+valid_expr = True
+try:
+    exec code
+except Exception, e:
+    out.close()
+    if str( e ).startswith( 'invalid syntax' ):
+        valid_expr = False
+        stop_err( 'Expression "%s" likely invalid. See tool tips, syntax and examples.' % expr )
+    else:
+        stop_err( str( e ) )
+
+if valid_expr:
+    out.close()
+    valid_lines = total_lines - skipped_lines
+    print 'Creating column %d with expression %s' % ( in_columns + 1, expr )
+    if valid_lines > 0:
+        print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines )
+    else:
+        print 'Possible invalid expression "%s" or non-existent column referenced. See tool tips, syntax and examples.' % expr
+    if skipped_lines > 0:
+        print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line )