Use logger instead of direct print to stderr

python/orgasm/assembler/_assembler.pyx

@@ -6,10 +6,10 @@ from orgasm.indexer._orgasm cimport *
 from ._asmbgraph cimport *
 from ._assembler cimport *
 from orgasm.graph._graphmultiedge cimport *
-
 from functools import reduce
 
 from orgasm.apps.progress cimport ProgressBar 
+from orgasm.apps.config cimport getConfiguration 
 from orgasm.utils.dna cimport reverseComplement
 import math
 
@@ -219,10 +219,8 @@ cpdef dict buildstem(Assembler assembler,
                   }
             
     if circle:
-        print(" Circle : %6d bp coverage : %6dx" % 
-              (length,int(w)),
-              file=sys.stderr
-             ) 
+        getConfiguration()['orgasm']['logger'].info(" Circle : %6d bp coverage : %6dx" % 
+              (length,int(w))) 
         
     return s   
 
@@ -249,7 +247,10 @@ cdef class CompactAssembling(DiGraphMultiEdge):
         cdef double minweight
         cdef AsmbGraph graph
         cdef dict stem
+        cdef dict config=getConfiguration()
         
+        logger = config['orgasm']['logger']
+         
         DiGraphMultiEdge.__init__(self,'compact')
         
         self._paths={}
@@ -262,7 +263,7 @@ cdef class CompactAssembling(DiGraphMultiEdge):
 
 
         if verbose:
-            print("Compacting graph :",file=sys.stderr)
+            logger.info("Compacting graph :")
         else:
             progress = ProgressBar(lgraph,
                                    head="Compacting graph",
@@ -282,17 +283,15 @@ cdef class CompactAssembling(DiGraphMultiEdge):
                 minweight=weight
 
             if verbose:
-                print(" Stem  : %6d bp (total : %6d) coverage : %6.2f" % (stem['length'],
-                                                                          lcontig,
-                                                                          weight),
-                      file=sys.stderr)
+                logger.info(" Stem  : %6d bp (total : %6d) coverage : %6.2f" % (stem['length'],
+                                                                                lcontig,
+                                                                                weight))
             else:
                 progress(lcontig)
            
         self.setStemid()            
              
-        print("\nMinimum stem coverage = %d" % int(minweight),
-              file=sys.stderr)
+        logger.info("Minimum stem coverage = %d" % int(minweight))
         
         
 
@@ -593,20 +592,23 @@ cdef class Assembler:
         cdef int32_t   i                                # @DuplicatedSignature
         cdef set       ep
         cdef set       sp
-                    
+                   
         graph=self.graph
 
         cd=0    
         d=1
             
-        print('',file=sys.stderr)
+        if sys.stderr.isatty():
+            print('',file=sys.stderr)
         
         while d > 0:
             d=0
+            
             for i in self.endNodeSet(alllink=alllink):
-                print("Remaining edges : %d node : %d" % (graph.edgeCount(),len(graph)),
-                      end='\r',
-                      file=sys.stderr)
+                if sys.stderr.isatty():
+                    print("Remaining edges : %d node : %d" % (graph.edgeCount(),len(graph)),
+                          end='\r',
+                          file=sys.stderr)
                 d+=deleteBranch(graph,[i],maxlength)
             cd+=d
             
@@ -620,9 +622,10 @@ cdef class Assembler:
             except KeyError:
                 pass
             
-        print ("Remaining edges : %d node : %d" % (graph.edgeCount(),len(graph)),
-               end='\r',
-               file=sys.stderr)
+        if sys.stderr.isatty():
+            print ("Remaining edges : %d node : %d" % (graph.edgeCount(),len(graph)),
+                   end='\r',
+                   file=sys.stderr)
 
         return cd