Cleaner stderr prints

python/obitools3/commands/align.pyx

@@ -255,8 +255,8 @@ def run(config):
     # Save command config in output DMS comments
     o_dms.record_command_line(command_line)
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_dms[final_o_view_name]))
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
     # If the two input DMS are different, delete the temporary input view in the first input DMS
     if i_dms_2 and i_dms != i_dms_2:
@@ -269,4 +269,6 @@ def run(config):
         o_dms.close()
     
     i_dms.close()
+    
+    logger("info", "Done.")
   

python/obitools3/commands/alignpairedend.pyx

@@ -226,6 +226,9 @@ def run(config):
     
         i+=1
 
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
     if kmer_ali :
         aligner.free()
 
@@ -234,11 +237,13 @@ def run(config):
     view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
     output[0].record_command_line(command_line)
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(view))
+    #print(repr(view), file=sys.stderr)
     
     input[0].close()
     if two_views:
         rinput[0].close()
     output[0].close()
 
+    logger("info", "Done.")
+    

python/obitools3/commands/annotate.pyx

@@ -356,6 +356,9 @@ def run(config):
 
     except Exception, e:
         raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
+
+    pb(i, force=True)
+    print("", file=sys.stderr)
     
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
@@ -367,12 +370,13 @@ def run(config):
     o_view.write_config(config, "annotate", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
     output[0].record_command_line(command_line)
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_view))
+    #print(repr(o_view), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(o_dms, imported_view_name)
         o_dms.close()
     i_dms.close()
-    
+
+    logger("info", "Done.")

python/obitools3/commands/build_ref_db.pyx

@@ -91,8 +91,8 @@ def run(config):
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_dms[final_o_view_name]))
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary result view in the input DMS
     if i_dms != o_dms:
@@ -101,3 +101,5 @@ def run(config):
     
     i_dms.close()
 
+    logger("info", "Done.")
+    

python/obitools3/commands/clean.pyx

@@ -111,8 +111,8 @@ def run(config):
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_dms[final_o_view_name]))
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary result view in the input DMS
     if i_dms != o_dms:
@@ -120,3 +120,5 @@ def run(config):
         o_dms.close()
     
     i_dms.close()
+
+    logger("info", "Done.")

python/obitools3/commands/ecopcr.pyx

@@ -194,8 +194,9 @@ def run(config):
     free(restrict_to_taxids_p)
     free(ignore_taxids_p)
     
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_dms[o_view_name]))
+    #print(repr(o_dms[o_view_name]), file=sys.stderr)
 
     o_dms.close()
 
+    logger("info", "Done.")

python/obitools3/commands/ecotag.pyx

@@ -115,8 +115,8 @@ def run(config):
     # Save command config in DMS comments
     o_dms.record_command_line(command_line)
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_dms[final_o_view_name]))
+    #print(repr(o_dms[final_o_view_name]), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary result view in the input DMS
     if i_dms != o_dms:
@@ -124,3 +124,6 @@ def run(config):
         o_dms.close()
     
     i_dms.close()
+    
+    logger("info", "Done.")
+

python/obitools3/commands/export.pyx

@@ -9,6 +9,7 @@ from obitools3.dms.obiseq import Nuc_Seq
 from obitools3.apps.optiongroups import addMinimalInputOption, \
                                         addExportOutputOption
 
+import sys
 
 __title__="Export a view to a different file format"
 
@@ -56,10 +57,13 @@ def run(config):
             break
         i+=1
 
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
     # TODO save command in input dms?
     
     output_object.close()
     iview.close()
     input[0].close()
 
-    logger("info", "obi export: Done")
+    logger("info", "Done.")

python/obitools3/commands/grep.pyx

@@ -314,6 +314,9 @@ def run(config):
         if good :
             selection.append(i)
 
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
     # Create output view with the line selection
     try:
         o_view = selection.materialize(o_view_name)
@@ -337,11 +340,13 @@ def run(config):
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
         o_view = o_dms[o_view_name_final]
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_view))
+    #print(repr(o_view), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(i_dms, o_view_name)
         o_dms.close()
     i_dms.close()
+
+    logger("info", "Done.")

python/obitools3/commands/head.pyx

@@ -72,7 +72,10 @@ def run(config):
     for i in range(n):
         pb(i)
         selection.append(i)
-    
+
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
     # Create output view with the line selection
     try:
         o_view = selection.materialize(o_view_name)
@@ -91,8 +94,8 @@ def run(config):
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
         o_view = o_dms[o_view_name_final]
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_view))
+    #print(repr(view), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
@@ -100,3 +103,4 @@ def run(config):
         o_dms.close()
     i_dms.close()
     
+    logger("info", "Done.")

python/obitools3/commands/ngsfilter.pyx

@@ -581,6 +581,9 @@ def run(config):
     except Exception, e:
         raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
     
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
     o_view.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
@@ -589,8 +592,8 @@ def run(config):
     unidentified.comments["info"] = "View containing sequences categorized as unidentified by the ngsfilter command"
     output[0].record_command_line(command_line)
     
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_view))
+    #print(repr(o_view), file=sys.stderr)
 
     input[0].close()
     output[0].close()
@@ -598,3 +601,4 @@ def run(config):
     unidentified_input[0].close()
     aligner.free()
 
+    logger("info", "Done.")

python/obitools3/commands/sort.pyx

@@ -109,6 +109,9 @@ def run(config):
     for k in keys:  # TODO order?
         selection.sort(key=lambda line_idx: line_cmp(i_view[line_idx], k, pb(line_idx)), reverse=config['sort']['reverse'])
 
+    pb(len(i_view), force=True)
+    print("", file=sys.stderr)
+
     # Create output view with the sorted line selection
     try:
         o_view = selection.materialize(o_view_name)
@@ -129,11 +132,13 @@ def run(config):
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
         o_view = o_dms[o_view_name_final]
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_view))
+    #print(repr(o_view), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(i_dms, o_view_name)
         o_dms.close()
     i_dms.close()
+
+    logger("info", "Done.")

python/obitools3/commands/stats.pyx

@@ -11,6 +11,7 @@ from obitools3.dms.capi.obiview cimport COUNT_COLUMN
 from functools import reduce
 import math
 import time
+import sys
  
 
 __title__="Compute basic statistics for attribute values."
@@ -199,6 +200,9 @@ def run(config):
                     values[var][category]=[]
                 values[var][category].append(v)    
 
+    pb(i, force=True)
+    print("", file=sys.stderr)
+    
     mini, lmini = minimum(values, config['stats'])
     maxi, lmaxi = maximum(values, config['stats'])
     avg, lavg = mean(values, config['stats'])
@@ -258,5 +262,4 @@ def run(config):
 
     input[0].close()
     
-    
+    logger("info", "Done.")
-    

python/obitools3/commands/tail.pyx

@@ -73,6 +73,9 @@ def run(config):
         pb(i)
         selection.append(i)
 
+    pb(i, force=True)
+    print("", file=sys.stderr)
+
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
     comments = View.get_config_dict(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
@@ -95,8 +98,8 @@ def run(config):
         View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
         o_view = o_dms[o_view_name_final]
 
-    print("\n")
+    #print("\n\nOutput view:\n````````````", file=sys.stderr)
-    print(repr(o_view))
+    #print(repr(o_view), file=sys.stderr)
 
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
@@ -104,3 +107,4 @@ def run(config):
         o_dms.close()
     i_dms.close()
     
+    logger("info", "Done.")

python/obitools3/parsers/embl.pyx

@@ -115,9 +115,7 @@ def emblIterator_file(lineiterator,
         line = next(iterator)
     else:
         line = firstline       
-        
+            
-    DONECOUNT=0
-        
     while True:
         
         if ionly >= 0 and read >= ionly-1:
@@ -154,11 +152,7 @@ def emblIterator_file(lineiterator,
             break
                 
         seq = emblParser(entry)
-        
+                
-        if DONECOUNT%10000 == 0:
-            print(DONECOUNT, "\n")
-        DONECOUNT+=1
-        
         yield seq
         read+=1