diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx index 470cfcf..86b48c4 100644 --- a/python/obitools3/commands/import.pyx +++ b/python/obitools3/commands/import.pyx @@ -12,6 +12,7 @@ from obitools3.dms.view.view cimport View from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.column.column cimport Column from obitools3.dms.obiseq cimport Nuc_Seq +from obitools3.dms import DMS from obitools3.utils cimport tobytes, \ get_obitype, \ @@ -82,6 +83,7 @@ def run(config): cdef bytes NA_value global obi_errno + DMS.obi_atexit() logger("info","obi import : imports file into an DMS") @@ -238,6 +240,6 @@ def run(config): print("\n") print(view.__repr__()) - input[0].close() # TODO + input[0].close() # TODO ? output[0].close() diff --git a/python/obitools3/commands/less.pyx b/python/obitools3/commands/less.pyx index 5d578bd..08a04e7 100644 --- a/python/obitools3/commands/less.pyx +++ b/python/obitools3/commands/less.pyx @@ -2,6 +2,7 @@ from obitools3.apps.optiongroups import addSequenceInputOption from obitools3.uri.decode import open_uri +from obitools3.dms import DMS __title__="Less equivalent" @@ -25,7 +26,9 @@ def run(config): cdef object entries cdef int n - + + DMS.obi_atexit() + input = open_uri(config['obi']['inputURI']) entries = input[1] diff --git a/python/obitools3/commands/uniq.pyx b/python/obitools3/commands/uniq.pyx index 189e34c..9cf65fd 100644 --- a/python/obitools3/commands/uniq.pyx +++ b/python/obitools3/commands/uniq.pyx @@ -1,7 +1,7 @@ #cython: language_level=3 from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport -from obitools3.dms.dms cimport DMS +from obitools3.dms import DMS from obitools3.dms.view.view cimport View, Line from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS from obitools3.dms.column.column cimport Column, Column_line @@ -44,6 +44,7 @@ def addOptions(parser): "used to group sequences before dereplication " "(option can be used several times).") +# TODO discuss # group.add_argument('--prefix', '-p', # action="store_true", dest="uniq:prefix", # default=False, @@ -400,7 +401,6 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, li merge_taxonomy_classification(o_view, taxonomy) - def run(config): cdef tuple input @@ -410,14 +410,16 @@ def run(config): cdef View_NUC_SEQS entries cdef View_NUC_SEQS o_view cdef ProgressBar pb - + + DMS.obi_atexit() + logger("info","obi uniq") input = open_uri(config['obi']['inputURI']) if input[2] != View_NUC_SEQS: raise NotImplementedError('obi uniq only works on NUC_SEQS views') - + output = open_uri(config['obi']['outputURI'], input=False, newviewtype=View_NUC_SEQS) @@ -434,14 +436,8 @@ def run(config): # Initialize the progress bar pb = ProgressBar(len(entries), config, seconde=5) - -# TODO -# if options.prefix: -# usm = uniqPrefixSequence -# else: - usm = uniq_sequences - usm(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories']) + uniq_sequences(entries, o_view, pb, mergedKeys_list=config['uniq']['merge'], taxonomy=taxo, mergeIds=config['uniq']['mergeids'], categories=config['uniq']['categories']) print("\n") print(repr(o_view))