Minor fixes

python/obitools3/commands/alignpairedend.pyx

@@ -28,14 +28,14 @@ def addOptions(parser):
  
     group.add_argument('-f', '--forward-reads',
                      action="store", dest="alignpairedend:forward",
-                     metavar="<FILENAME>",
+                     metavar="<URI>",
                      default=None,
                      type=str,
                      help="URI to the forward reads")
 
     group.add_argument('-r', '--reverse-reads',
                      action="store", dest="alignpairedend:reverse",
-                     metavar="<FILENAME>",
+                     metavar="<URI>",
                      default=None,
                      type=str,
                      help="URI to the reverse reads")
@@ -56,6 +56,8 @@ def addOptions(parser):
                      help="Minimum score for keeping alignments")
 
 
+# TODO declarations, cdef, imports
+
 la = QSolexaReverseAssemble()
 ra = QSolexaRightReverseAssemble()
 def buildAlignment(Nuc_Seq_Stored direct, Nuc_Seq_Stored reverse):

python/obitools3/commands/ngsfilter.pyx

@@ -5,16 +5,13 @@ from obitools3.dms import DMS
 from obitools3.dms.view import RollbackException
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 from obitools3.dms.column.column cimport Column, Column_line
-from obitools3.dms.capi.obiview cimport QUALITY_COLUMN, COUNT_COLUMN, NUC_SEQUENCE_COLUMN, ID_COLUMN
-from obitools3.dms.capi.obitypes cimport OBI_INT, OBI_STR, index_t, OBI_QUAL
 from obitools3.apps.optiongroups import addSequenceInputOption, addMinimalOutputOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
 from obitools3.align._freeendgapfm import FreeEndGapFullMatch
-from obitools3.dms.obiseq cimport Nuc_Seq, Nuc_Seq_Stored
+from obitools3.dms.obiseq cimport Nuc_Seq
 from functools import reduce, cmp_to_key
 import math
-from curses.ascii import SO
 
 
 __title__="Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers"
@@ -388,6 +385,9 @@ def run(config):
     except Exception, e:
         raise RollbackException("obi ngsfilter error, rollbacking views: "+str(e), o_view, unidentified)
 
+    print("\n")
+    print(repr(o_view))
+
     input[0].close()
     output[0].close()
     info_input[0].close()