diff --git a/pyradar/pyradar.h b/pyradar/pyradar.h
index ee0c753..aa6503b 100644
--- a/pyradar/pyradar.h
+++ b/pyradar/pyradar.h
@@ -5,5 +5,10 @@
  * 
  * */
 
-int radar_run_from_files( const char * seq, const char * mali, const char * lfasta1, const char * lfasta2 );
-void radar_setLogLevel( int f);
+int radar_run_from_files(const char * seq,
+			 const char * mali,
+			 const char * lfasta1,
+			 const char * lfasta2,
+			 int random_seed);
+
+void radar_setLogLevel(int f);
diff --git a/pyradar/pyradar.pyx b/pyradar/pyradar.pyx
index fc4c42e..d860bab 100644
--- a/pyradar/pyradar.pyx
+++ b/pyradar/pyradar.pyx
@@ -3,11 +3,15 @@ Pyrex extension classes used by 'radar.py'.
 """
 
 cdef extern from "pyradar.h":
-	int radar_run_from_files( char *, char *, char *, char * )
-	void radar_setLogLevel( int )
+	int radar_run_from_files(char *, char *, char *, char *, unsigned int)
+	void radar_setLogLevel(int)
     
-def run_from_files( filename_sequence, filename_mali, filename_lfasta, filename_lfasta2 ):
-	return radar_run_from_files( filename_sequence, filename_mali, filename_lfasta, filename_lfasta2 )
+def run_from_files(filename_sequence, filename_mali,
+                   filename_lfasta, filename_lfasta2,
+                   random_seed):
+	return radar_run_from_files(filename_sequence, filename_mali,
+                                    filename_lfasta, filename_lfasta2,
+                                    random_seed)
     
 def setLogLevel(v):
 	"""set the logging level."""
diff --git a/scripts/radar.py b/scripts/radar.py
index 6edb713..3ec86bd 100644
--- a/scripts/radar.py
+++ b/scripts/radar.py
@@ -2,102 +2,99 @@
 ####
 ####
 ##
-## Project PairsDB
+# Project PairsDB
 ##
-## Copyright (C) 2002 Andreas Heger All rights reserved
+# Copyright (C) 2002 Andreas Heger All rights reserved
 ##
-## Author: Andreas Heger <heger@ebi.ac.uk>
+# Author: Andreas Heger <heger@ebi.ac.uk>
 ##
-## $Id: WrapperRadar.py,v 1.1.1.1 2002/07/02 10:46:58 heger Exp $
+# $Id: WrapperRadar.py,v 1.1.1.1 2002/07/02 10:46:58 heger Exp $
 ##
 ##
 ####
 ####
-USAGE="""radar.py [OPTIONS] filenames
+
+import gzip
+import logging
+import optparse
+import os
+import pyradar
+import re
+import shutil
+import string
+import subprocess
+import sys
+import tempfile
+
+USAGE = """radar.py [OPTIONS] filenames
 
 run radar on one or more fasta-formatted files.
 """
 
-import re, sys, os, string, tempfile, optparse, shutil, types, subprocess
-
 rx_repeat = re.compile("^\s*(\d+)\-\s*(\d+)\s+\(\s*(\S+)\/\s*(\S+)\)\s+(\S+)")
 
-##----------------------------------------------------------------------------------------
+# ----------------------------------------------------------------------------------------
 DEBUG = 0
 
-import pyradar
 
 class RadarRepeat:
-    def __init__( self, file):
+
+    def __init__(self, file):
         """Build members from a file."""
 
-        ## read up to header
+        # read up to header
         while 1:
             line = file.readline()
-            if not line: break
-            
-            if line[0:3] == "No.": break
+            if not line:
+                break
 
-        ## read header
+            if line[0:3] == "No.":
+                break
+
+        # read header
         line = file.readline()
-        data = string.split( line, "|")
+        data = string.split(line, "|")
 
-        self.mNRepeats = string.atoi(string.strip(data[0]))
-        self.mScore    = string.atof(string.strip(data[1]))
-        self.mLength   = string.atoi(string.strip(data[2]))
-        self.mDiagonal = string.atoi(string.strip(data[3]))
-        self.mBW_from  = string.atoi(string.strip(data[4]))
-        self.mBW_to    = string.atoi(string.strip(data[5]))
-        self.mLevel    = string.atoi(string.strip(data[6]))
+        self.nrepeats = string.atoi(string.strip(data[0]))
+        self.score = string.atof(string.strip(data[1]))
+        self.length = string.atoi(string.strip(data[2]))
+        self.diagonal = string.atoi(string.strip(data[3]))
+        self.bw_from = string.atoi(string.strip(data[4]))
+        self.bw_to = string.atoi(string.strip(data[5]))
+        self.level = string.atoi(string.strip(data[6]))
 
-        ## read single repeats
+        # read single repeats
         file.readline()
 
-        self.mRepeatUnits = []
+        self.repeat_units = []
         while 1:
             line = file.readline()
-            if not line: break
-            
-            result = rx_repeat.search( line )
+            if not line:
+                break
 
-            if not result: break
-            
-            self.mRepeatUnits.append( result.groups())
-        
-    def GetBWFrom(self):
-        return self.mBW_from
-    def GetBWTo(self):
-        return self.mBW_to
-    def GetNRepeats(self):
-        return self.mNRepeats
-    def GetDiagonal(self):
-        return self.mDiagonal
-    def GetLength(self):
-        return self.mLength
-    def GetScore(self):
-        return self.mScore
-    def GetLevel(self):
-        return self.mLevel
-    def GetRepeatUnits( self ):
-        return self.mRepeatUnits
-    
-    def Print( self ):
-        print  string.join ( 
-            map( str, (self.mNRepeats, self.mScore, self.mLength, self.mLevel)) ,
-            "\t" )
-        print self.mRepeatUnits
-
-    ##------------------------------------------------------------------------            
-    def BuildResult( self, file ):
+            result = rx_repeat.search(line)
+
+            if not result:
+                break
+
+            self.repeat_units.append(result.groups())
+
+    def __str__(self):
+        return "\t".join(
+            map(str, (self.nrepeats, self.score, self.length, self.level)) +\
+            "\n".join(self.repeat_units))
+
+    def build_result(self, file):
         """parse the output file and return a tuple of repeats.
         """
 
         repeats = []
-        
+
         while 1:
             line = file.readline()
-            if not line: break
-            
+            if not line:
+                break
+
             if line[:-1] == "repeatfinder finished without problems":
                 break
             elif line[:-1] == "Not enough dots given":
@@ -106,139 +103,156 @@ def BuildResult( self, file ):
                 break
             else:
                 try:
-                    repeats.append( RadarRepeat( file ))
+                    repeats.append(RadarRepeat(file))
                 except ValueError:
                     break
 
         return tuple(repeats)
 
-##------------------------------------------------------------
-def multiple_fasta_iterator (filenames, regex_identifier = None ):
+
+def multiple_fasta_iterator(filenames, regex_identifier=None):
     """iterate over multiple fasta files."""
-    
+
     identifier = None
-        
+
     for filename in filenames:
 
         if filename[-3:] == ".gz":
-            infile = gzip.open( filename, "r" )
+            infile = gzip.open(filename, "r")
         elif filename == "-":
             infile = sys.stdin
         else:
-            infile = open( filename, "r")
+            infile = open(filename, "r")
 
         for line in infile:
 
-            if line[0] == "#":  continue
+            if line[0] == "#":
+                continue
 
-            if line[0] == ">" :
+            if line[0] == ">":
 
                 if identifier:
                     yield identifier, "".join(fragments)
-                    
+
                 if regex_identifier:
                     try:
-                        identifier = re.search(regex_identifier, line[1:-1]).groups()[0]
+                        identifier = re.search(
+                            regex_identifier, line[1:-1]).groups()[0]
                     except AttributeError:
-                        raise "could not parse identifier from line %s - check the input" % line[1:-1]
+                        raise "could not parse identifier from line %s - check the input" % line[
+                            1:-1]
                 else:
                     identifier = re.split("\s", line[1:-1])[0]
                 fragments = []
             else:
-                fragments.append (re.sub( "\s", "", line.strip() ) )
+                fragments.append(re.sub("\s", "", line.strip()))
 
-        if filename != "-": infile.close()
+        if filename != "-":
+            infile.close()
 
     if identifier:
         yield identifier, "".join(fragments)
     raise StopIteration
 
-def runLFasta( filename_sequence, filename_output, lfasta_options ):
-    
-    retcode = subprocess.call( "lfasta %s %s %s > %s " % \
-                               (filename_sequence, filename_sequence, lfasta_options, filename_output),
-                               stderr=subprocess.PIPE,
-                               shell=True)
+
+def run_lfasta(filename_sequence, filename_output, lfasta_options):
+
+    retcode = subprocess.call("lfasta %s %s %s > %s " %
+                              (filename_sequence, filename_sequence,
+                               lfasta_options, filename_output),
+                              stderr=subprocess.PIPE,
+                              shell=True)
     if retcode != 0:
-        raise IOError( "error while running lfasta: code = %i" % retcode )    
+        raise IOError("error while running lfasta: code = %i" % retcode)
+
 
 def main():
 
-    parser = optparse.OptionParser( version = "%prog version: $Id$", usage = USAGE )
+    parser = optparse.OptionParser(version="%prog version: $Id$", usage=USAGE)
 
-    parser.add_option( "-a", "--filename-fasta", dest="filename_fasta", type="string", action="append",
-                       help="filename with fasta sequence [default=%default]")
+    parser.add_option("-a", "--filename-fasta", dest="filename_fasta", type="string", action="append",
+                      help="filename with fasta sequence [default=%default]")
 
     parser.add_option("-v", "--verbose", dest="loglevel", type="int",
-                      help="loglevel [%default]. The higher, the more output." )
+                      help="loglevel [%default]. The higher, the more output.")
 
     parser.add_option("-L", "--log", dest="stdlog", type="string",
                       help="file with logging information [default = stdout].",
-                      metavar = "FILE"  )
-    
+                      metavar="FILE")
+
     parser.add_option("-E", "--error", dest="stderr", type="string",
                       help="file with error information [default = stderr].",
-                      metavar = "FILE"  )
-    
+                      metavar="FILE")
+
     parser.add_option("-S", "--stdout", dest="stdout", type="string",
                       help="file where output is to go [default = stdout].",
-                      metavar = "FILE"  )
-        
+                      metavar="FILE")
+
+    parser.add_option("--keep-temp", dest="keep_temp", action="store_true",
+                      help="keep temporary directory [%default].",
+                      metavar="FILE")
+
+    parser.add_option("--random-seed", dest="random_seed", type="int",
+                      help="set random seed to value. Set to 0 to use random seed [%default].")
+
     parser.set_defaults(
-                        stderr = sys.stderr,
-                        stdout = sys.stdout, 
-                        stdlog = sys.stdout,
-                        filename_fasta = [],
-                        loglevel = 0,
-                        tmpdir = "/tmp",
-                        regex_identifier = "^(\S+)" )
+        stderr=sys.stderr,
+        stdout=sys.stdout,
+        stdlog=sys.stdout,
+        filename_fasta=[],
+        loglevel=0,
+        tmpdir="/tmp",
+        keep_temp=False,
+        random_seed=0,
+        regex_identifier="^(\S+)")
 
     (options, args) = parser.parse_args()
 
-    if options.stdout != sys.stdout: 
+    logging.basicConfig(level=logging.INFO)
+    
+    if options.stdout != sys.stdout:
         options.stdout = open(options.stdout, "w")
     if options.stderr != sys.stderr:
         options.stderr = open(options.stderr, "w")
     if options.stdlog != sys.stdout:
-        options.stdlog = open(options.stdlog, "a") 
- 
+        options.stdlog = open(options.stdlog, "a")
+
     options.filename_fasta += args
-    
+
     if len(options.filename_fasta) == 0:
         options.filename_fasta.append("-")
-    
-    pyradar.setLogLevel( options.loglevel )
-    
-    iterator = multiple_fasta_iterator( options.filename_fasta,
-                                        regex_identifier = options.regex_identifier )
-    
-    for identifier, sequence in iterator:
-    
-        options.stdout.write(">%s\n" % identifier )
-        tmpdir = tempfile.mkdtemp( prefix = options.tmpdir + "/" )
-        filename_sequence = tmpdir + "/seq"
-        filename_lfasta1 = tmpdir + "/lfasta1"
-        filename_lfasta2 = tmpdir + "/lfasta2"            
-        outfile = open(filename_sequence, "w")
-        outfile.write(sequence)
-        outfile.close()
-        
-        runLFasta( filename_sequence, filename_lfasta1, "")
-        runLFasta( filename_sequence, filename_lfasta2, "-f -12 -g -2 -s 250" )
-        
-        pyradar.run_from_files( filename_sequence, 
-                                filename_sequence,
-                                filename_lfasta1, 
-                                filename_lfasta2 )
-        
-        shutil.rmtree( tmpdir )
-    
-if __name__ == '__main__':
-    sys.exit(main())
-    
-
-
 
+    pyradar.setLogLevel(options.loglevel)
 
+    iterator = multiple_fasta_iterator(
+        options.filename_fasta,
+        regex_identifier=options.regex_identifier)
 
+    for identifier, sequence in iterator:
+        
+        options.stdout.write(">%s\n" % identifier)
+        tmpdir = tempfile.mkdtemp(prefix=options.tmpdir + "/")
+        filename_sequence = os.path.join(tmpdir, "seq")
+        filename_lfasta1 = os.path.join(tmpdir, "lfasta1")
+        filename_lfasta2 = os.path.join(tmpdir, "lfasta2")
+        with open(filename_sequence, "w") as outf:
+            outf.write(sequence)
+
+        run_lfasta(filename_sequence, filename_lfasta1, "")
+        run_lfasta(filename_sequence, filename_lfasta2, "-f -12 -g -2 -s 250")
+
+        pyradar.run_from_files(filename_sequence,
+                               filename_sequence,
+                               filename_lfasta1,
+                               filename_lfasta2,
+                               random_seed=options.random_seed)
+
+        if not options.keep_temp:
+            shutil.rmtree(tmpdir)
+        else:
+            logging.info("temporary directory {} will not be deleted".format(
+                tmpdir))
 
+            
+if __name__ == '__main__':
+    sys.exit(main())
diff --git a/setup.py b/setup.py
index b99c456..a6e2856 100644
--- a/setup.py
+++ b/setup.py
@@ -1,29 +1,30 @@
 #!/usr/bin/env python
 
-import os, glob, sys, subprocess
-import ez_setup
-ez_setup.use_setuptools()
+import glob
+import sys
+import subprocess
+import setuptools
 
 from distutils.core import setup
 from distutils.extension import Extension
 
-## check if cython exists
+# check if cython exists
 try:
     from Cython.Distutils import build_ext
 except:
     print """Cython not installed. Please install cython from
     http://cython.org.
 """
-    sys.exit (1)
+    sys.exit(1)
 
-## check if lfasta exitst
-retcode = subprocess.call( "which lfasta",
-                           shell=True)
+# check if lfasta exitst
+retcode = subprocess.call("which lfasta",
+                          shell=True)
 if retcode != 0:
     print """WARNING: could not find lfasta in your path.
 
-Please download the source code of W.R. Pearson's fasta package and build
-lfasta using the following commands:
+Please download the source code of W.R. Pearson's fasta package and
+build lfasta using the following commands:
 
 mkdir fasta2
 cd fasta2
@@ -35,27 +36,26 @@
 Copy the lfasta executable somewhere into your path.
 """
 
-c_sources = [ x for x in glob.glob( "src/*.c" ) if x not in "src/main.c" ]
-                   
+c_sources = [x for x in glob.glob("src/*.c") if x not in "src/main.c"]
+
 # build the interface
 pyradar = Extension(
     "pyradar",                   # name of extension
-    [ "pyradar/pyradar.pyx", ] + c_sources, 
-      library_dirs=[],
-      libraries=[],              
-      language="c",               
-    )
+    ["pyradar/pyradar.pyx", ] + c_sources,
+    library_dirs=[],
+    libraries=[],
+    language="c",
+)
 
 setup(name='Radar',
-      version='1.1.3',
+      version='1.2',
       description='RADAR - Rapid Automatic Detection and Alignment of Repeats',
-      author='Andreas Heger',
-      author_email='andreas.heger@helsinki.fi',
-      url='http://wwwfgu.anat.ox.ac.uk/~andreas',
-      package_dir = {}, 
-      packages = [], 
-      scripts=['scripts/radar.py',],
-      ext_modules=[ pyradar ],
-      cmdclass = {'build_ext': build_ext}
-     )
-    
\ No newline at end of file
+      author='Andreas Heger & Liisa Holm',
+      author_email='andreas.heger@gmail.com',
+      url='https://github.com/AndreasHeger/radar',
+      package_dir={},
+      packages=[],
+      scripts=['scripts/radar.py', ],
+      ext_modules=[pyradar],
+      cmdclass={'build_ext': build_ext}
+      )
diff --git a/src/radar.c b/src/radar.c
index 3424b9c..31a9a1e 100644
--- a/src/radar.c
+++ b/src/radar.c
@@ -2148,10 +2148,11 @@ extern char globalresult[MAXRESULTSIZE];
 }
 
 int radar_run_from_files( 
-		const char * filename_sequence,
-		const char * filename_ma,
-		const char * filename_lfasta,
-		const char * filename_lfasta2)
+			 const char * filename_sequence,
+			 const char * filename_ma,
+			 const char * filename_lfasta,
+			 const char * filename_lfasta2,
+			 unsigned int random_seed)
 {
 	int lprofile;
 	PROFILECOLUMN *profile;
@@ -2167,7 +2168,12 @@ int radar_run_from_files(
 	WellcomeMsg();
 	globalresult[0] = '\0'; 
 
-	/* read sequence and allocate memory for the masked sequence -------------------------------------------------------*/
+	if (random_seed != 0) 
+	    srand(random_seed);
+	else
+	    srand((unsigned int)clock());
+
+	/* read sequence and allocate memory for the masked sequence -----*/
 	if (verbose > LL1) printf("Reading sequence...");
 	lsequence = ReadSequence( filename_sequence, &sequence );
 	if (verbose > LL1) printf("Done (length=%i)\n", lsequence);
diff --git a/src/radar.h b/src/radar.h
index a0de6aa..bcb3e6f 100644
--- a/src/radar.h
+++ b/src/radar.h
@@ -110,7 +110,7 @@ int CountAndScoreRepeats();
 void CalculateZScore();
 
 
-int radar_run_from_files( const char *, const char *, const char *, const char *);
-void radar_setLogLevel( int );
+int radar_run_from_files(const char *, const char *, const char *, const char *, unsigned int);
+void radar_setLogLevel(int);
 
-#endif
\ No newline at end of file
+#endif
diff --git a/src/repeatstatistics.c b/src/repeatstatistics.c
index 5052939..abc0cf5 100644
--- a/src/repeatstatistics.c
+++ b/src/repeatstatistics.c
@@ -119,7 +119,6 @@ double *mean, *standard_deviation;
     CALCTYPE *scores      = Malloc( iterations * sizeof(CALCTYPE));
     int i;
 
-    srand((unsigned int)clock());
     /* get scores for iterations alignments of shuffled sequences against profile---------------------------------------------------*/
     for (i = 0; i < iterations; i++) {
 	ShuffleSequence( rsequence, lsequence );