added printing of all parameter settings in Param object to statistics

BESST/Parameter.py

@@ -103,6 +103,12 @@ def __init__(self, parameter_mean_coverage=None, parameter_std_dev_coverage=None
         self.NO_ILP = NO_ILP
         self.FASTER_ILP = FASTER_ILP
 
+    def get_params(self):
+        output = "param\tvalue\n"
+        values = "".join([ "{0}\t{1}\n".format(attr, value) if value == None or type(value) in [bool, int,float, file] or len(value) < 5 else "" for attr, value in self.__dict__.items() if not callable(value)])
+        output += values
+        return output
+
 class counters(object):
     def __init__(self, param_count=None, param_non_unique=None, param_non_unique_for_scaf=None,
                  param_nr_of_duplicates=None, param_prev_obs1=None, param_prev_obs2=None,

runBESST

@@ -219,7 +219,10 @@ def main(options):
             shutil.copyfileobj(open("{0}/repeats.fa".format(param.output_directory, str(i+1) ), 'rb'), destination)
             destination.close()
             os.remove( "{0}/pass{1}/Scaffolds-pass{1}.fa".format(param.output_directory, str(i+1)) )
-
+
+        all_parameter_settings = param.get_params()  
+        print >> Information, all_parameter_settings
+
         param.first_lib = False   #not the first lib any more    
 
     if not options.separate_repeats: