fixes generate.py

generate.py

@@ -32,9 +32,9 @@ def generateOneText(infile, modelfile, reportfile):
 
     #begin processing
     cmdline = ['./gen_k_mixture_model', '--maximum-occurs-allowed', \
-                   config.getMaximumOccursAllowed(), \
+                   str(config.getMaximumOccursAllowed()), \
                    '--maximum-increase-rates-allowed', \
-                   config.getMaximumIncreaseRatesAllowed(), \
+                   str(config.getMaximumIncreaseRatesAllowed()), \
                    '--k-mixture-model-file', \
                    modelfile, infile + \
                    config.getSegmentPostfix()]
@@ -73,6 +73,16 @@ def handleOneIndex(indexpath, subdir, indexname):
     if 'GenerateModelEnd' in indexstatus:
         modelnum = indexstatus['GenerateModelEnd']
 
+    #clean up previous file
+    modeldir = os.path.join(config.getModelDir(), subdir, indexname)
+    modelfile = os.path.join( \
+        modeldir, config.getCandidateModelName(modelnum))
+    reportfile = modelfile + config.getReportPostfix()
+    if os.access(modelfile, os.F_OK):
+        os.unlink(modelfile)
+    if os.access(reportfile, os.F_OK):
+        os.unlink(reportfile)
+
     #begin processing
     indexfile = open(indexpath, 'r')
     for i, oneline in enumerate(indexfile.readlines()):
@@ -112,14 +122,7 @@ def handleOneIndex(indexpath, subdir, indexname):
             aggmodelsize = 0
             textnum = nexttextnum
             modelnum += 1
-            modeldir = os.path.join(config.getModelDir(), subdir, indexname)
-            modelfile = os.path.join( \
-                modeldir, config.getCandidateModelName(modelnum))
-            reportfile = modelfile + config.getReportPostfix()
-            if os.access(modelfile, os.F_OK):
-                os.unlink(modelfile)
-            if os.access(reportfile, os.F_OK):
-                os.unlink(reportfile)
+
             #save current progress in status file
             indexstatus['GenerateTextEnd'] = nexttextnum
             indexstatus['GenerateModelEnd'] = modelnum

lib/myconfig.py

@@ -78,6 +78,9 @@ def getMaximumOccursAllowed(self):
     def getMaximumIncreaseRatesAllowed(self):
         return 3.
 
+    def getReportPostfix(self):
+        return '.report'
+
     def getSegmentPostfix(self):
         return '.segmented'
 

lib/utils.py

@@ -1,3 +1,4 @@
+import io
 import os
 import json
 from myconfig import MyConfig
@@ -34,7 +35,7 @@ def write_file(outfile, data):
 
 def get_file_length(infile):
     f = open(infile, 'r')
-    f.seek(0, whence=io.SEEK_END)
+    f.seek(0, io.SEEK_END)
     length = f.tell()
     f.close()
     return length