--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/stats/gsummary.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,114 @@
+#!/usr/bin/env python
+
+import sys, re, tempfile
+from rpy import *
+# Older py compatibility
+try:
+    set()
+except:
+    from sets import Set as set
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def S3_METHODS( all="key" ):
+    Group_Math =  [ "abs", "sign", "sqrt", "floor", "ceiling", "trunc", "round", "signif",
+        "exp", "log", "cos", "sin", "tan", "acos", "asin", "atan", "cosh", "sinh", "tanh",
+        "acosh", "asinh", "atanh", "lgamma", "gamma", "gammaCody", "digamma", "trigamma",
+        "cumsum", "cumprod", "cummax", "cummin", "c" ]
+    Group_Ops = [ "+", "-", "*", "/", "^", "%%", "%/%", "&", "|", "!", "==", "!=", "<", "<=", ">=", ">", "(", ")", "~", "," ]
+    if all is "key":
+        return { 'Math' : Group_Math, 'Ops' : Group_Ops }
+
+def main():
+    try:
+        datafile = sys.argv[1]
+        outfile_name = sys.argv[2]
+        expression = sys.argv[3]
+    except: 
+        stop_err( 'Usage: python gsummary.py input_file ouput_file expression' )
+
+    math_allowed = S3_METHODS()[ 'Math' ]
+    ops_allowed = S3_METHODS()[ 'Ops' ]
+
+    # Check for invalid expressions
+    for word in re.compile( '[a-zA-Z]+' ).findall( expression ):
+        if word and not word in math_allowed: 
+            stop_err( "Invalid expression '%s': term '%s' is not recognized or allowed" %( expression, word ) )
+    symbols = set()
+    for symbol in re.compile( '[^a-z0-9\s]+' ).findall( expression ):
+        if symbol and not symbol in ops_allowed:
+            stop_err( "Invalid expression '%s': operator '%s' is not recognized or allowed" % ( expression, symbol ) )
+        else:
+            symbols.add( symbol )
+    if len( symbols ) == 1 and ',' in symbols:
+        # User may have entered a comma-separated list r_data_frame columns
+        stop_err( "Invalid columns '%s': this tool requires a single column or expression" % expression )
+
+    # Find all column references in the expression
+    cols = []
+    for col in re.compile( 'c[0-9]+' ).findall( expression ):
+        try:
+            cols.append( int( col[1:] ) - 1 )
+        except:
+            pass
+ 
+    tmp_file = tempfile.NamedTemporaryFile( 'w+b' )
+    # Write the R header row to the temporary file
+    hdr_str = "\t".join( "c%s" % str( col+1 ) for col in cols )
+    tmp_file.write( "%s\n" % hdr_str )
+    skipped_lines = 0
+    first_invalid_line = 0
+    i = 0
+    for i, line in enumerate( file( datafile ) ):
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ):
+            valid = True
+            fields = line.split( '\t' )
+            # Write the R data row to the temporary file
+            for col in cols:
+                try:
+                    float( fields[ col ] )
+                except:
+                    skipped_lines += 1
+                    if not first_invalid_line:
+                        first_invalid_line = i + 1
+                    valid = False
+                    break
+            if valid:
+                data_str = "\t".join( fields[ col ] for col in cols )
+                tmp_file.write( "%s\n" % data_str )
+    tmp_file.flush()
+
+    if skipped_lines == i + 1:
+        stop_err( "Invalid column or column data values invalid for computation.  See tool tips and syntax for data requirements." )
+    else:
+        # summary function and return labels
+        summary_func = r( "function( x ) { c( sum=sum( as.numeric( x ), na.rm=T ), mean=mean( as.numeric( x ), na.rm=T ), stdev=sd( as.numeric( x ), na.rm=T ), quantile( as.numeric( x ), na.rm=TRUE ) ) }" )
+        headings = [ 'sum', 'mean', 'stdev', '0%', '25%', '50%', '75%', '100%' ]
+        headings_str = "\t".join( headings )
+        
+        set_default_mode( NO_CONVERSION )
+        r_data_frame = r.read_table( tmp_file.name, header=True, sep="\t" )
+        
+        outfile = open( outfile_name, 'w' )
+
+        for col in re.compile( 'c[0-9]+' ).findall( expression ):
+            r.assign( col, r[ "$" ]( r_data_frame, col ) )
+        try:
+            summary = summary_func( r( expression ) )
+        except RException, s:
+            outfile.close()
+            stop_err( "Computation resulted in the following error: %s" % str( s ) )
+        summary = summary.as_py( BASIC_CONVERSION )
+        outfile.write( "#%s\n" % headings_str )
+        outfile.write( "%s\n" % "\t".join( [ "%g" % ( summary[ k ] ) for k in headings ] ) )
+        outfile.close()
+
+        if skipped_lines:
+            print "Skipped %d invalid lines beginning with line #%d.  See tool tips for data requirements." % ( skipped_lines, first_invalid_line )        
+
+if __name__ == "__main__": main()