obi export: made output to stdout and pipe in less possible

python/obitools3/commands/export.pyx

@@ -7,9 +7,11 @@ from obitools3.dms import DMS
 from obitools3.dms.obiseq import Nuc_Seq
 
 from obitools3.apps.optiongroups import addMinimalInputOption, \
-                                        addExportOutputOption
+                                        addExportOutputOption, \
+                                        addNoProgressBarOption
 
 import sys
+import io
 
 __title__="Export a view to a different file format"
 
@@ -18,6 +20,7 @@ def addOptions(parser):
     
     addMinimalInputOption(parser)
     addExportOutputOption(parser)
+    addNoProgressBarOption(parser)
 
 
 def run(config):
@@ -46,24 +49,33 @@ def run(config):
         raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
    
     # Initialize the progress bar
+    if config['obi']['noprogressbar']:
+        pb = None
+    else:
         pb = ProgressBar(len(iview), config, seconde=5)
     
     i=0
     for seq in iview :
+        if pb is not None:
             pb(i)
         try:
             writer(seq)
-        except StopIteration:
+        except (StopIteration, BrokenPipeError, IOError):
             break
         i+=1
 
+    if pb is not None:
         pb(i, force=True)
     print("", file=sys.stderr)
 
     # TODO save command in input dms?
     
+    if not BrokenPipeError and not IOError:
         output_object.close()
     iview.close()
     input[0].close()
 
     logger("info", "Done.")
+
+    if BrokenPipeError or IOError:
+        sys.stderr.close()